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Sample records for nsls infared microspectroscopy

  1. CHARACTERIZATION OF THE NEW NSLS INFARED MICROSPECTROSCOPY BEAMLINE U10B.

    SciTech Connect

    CARR,G.L.

    1999-07-19

    The first of several new infrared beamlines, built on a modified bending magnet port of the NSLS VUV ring, is now operational for mid-infrared microspectroscopy. The port simultaneously delivers 40 mrad by 40 mrad to two separate beamlines and spectrometer endstations designated U10A and U10B. The latter is equipped with a scanning infrared microspectrometer. The combination of this instrument and high brightness synchrotron radiation makes diffraction-limited microspectroscopy practical. This paper describes the beamline's performance and presents quantitative information on the diffraction-limited resolution.

  2. Characterization of the new NSLS infrared microspectroscopy beamline U10B

    SciTech Connect

    Carr, G.L.

    1999-07-19

    The first of several new infrared beamlines, built on a modified bending magnet port of the NSLS VUV ring, is now operational for mid-infrared microspectroscopy. The port simultaneously delivers 40 mrad by 40 mrad to two separate beamlines and spectrometer endstations designated U10A and U10B. The latter is equipped with a scanning infrared microspectrometer. The combination of this instrument and high brightness synchrotron radiation makes diffraction-limited microspectroscopy practical. This paper describes the beamline's performance and presents quantitative information on the diffraction-limited resolution.

  3. Microspectroscopy

    SciTech Connect

    Hirschfeld, T.

    1982-07-01

    The boom in electron and ion microbeam methods, with its overwhelming proliferation of new methods (and acronyms) and eager exploitation of every available technological advance, has tended to obscure the very wide usage of the corresponding optical methods. These outgrowths of the enormous field of visual optical microscopy are, however, quite alive and kicking, and their unique capabilities are becoming more appreciated as more and more advanced optical technology is being applied to the field. This review of optical microprobe techniques includes uv-VIS absorption techniques, fluorescence microspectroscopy, Raman measurements, and other microprobes such as the infrared ones, scatter, and the various partially optical methods. Also discussed are technological advances that may impact these fields. The natural place of microspectroscopy is shown to be as a higher discrimination, lower resolution companion of electron and ion beam microprobes.

  4. NSLS 2009 Activity Report

    SciTech Connect

    Nasta K.; Mona R.

    2009-05-01

    2009 was an incredibly exciting year for light sources at Brookhaven. The National Synchrotron Light Source (NSLS) hosted more than 2,200 visiting researchers, who, along with the about 50 members of our scientific staff, produced a total of 957 publications - about 20 percent of which appeared in premier journals. Covering topics ranging from Alzheimer's disease detection to ethanol-powered fuel cells, a sampling of these findings can be found in this Activity Report. We've also seen the resurfacing of some of our long-time users hard work. I was very proud to hear that two of the three recipients of the 2009 Nobel Prize in Chemistry have ties to the NSLS. Venki Ramakrishnan, a former employee in Brookhaven's biology department and long-time user of the NSLS, now at Cambridge University, and Thomas A. Steitz of Yale University, also a long-time NSLS user, shared the prize with Ada E. Yonath of the Weizmann Institute of Science for their work on the structure and function of the ribosome. In the late 1990s, Ramakrishnan and Steitz used protein crystallography at the NSLS to gather atomic-level images of two ribosome subunits: 30S (Ramakrishnan) and 50S (Steitz). Both laureates solved the high-resolution structures for these subunits based on this data. After struggling with a rough budget for several years, we received excellent funding, and then some, this year. In addition to NSLS operations funding, we received $3 million in funds from the American Recovery and Reinvestment Act (ARRA). We used that additional money for two exciting projects: construction of a full-field x-ray microscope and acquisition of several advanced x-ray detectors. The x-ray microscope will be able to image objects with a targeted spatial resolution of 30 nanometers. This capability will be particularly important for new initiatives in energy research and will prepare our users for the projected 1-nanometer resolution benchmark at the National Synchrotron Light Source II (NSLS-II). The

  5. NSLS-II INJECTION CONCEPT.

    SciTech Connect

    SHAFTAN, T.; PINAYEV, I.; ROSE, J.; WANG, X.J.; ET AL.

    2005-05-16

    Currently the facility upgrade project is in progress at the NSLS (at Brookhaven National Laboratory). The goal of the NSLS-II is a 3 GeV ultra-low-emittance storage ring that will increase radiation brightness by three orders of magnitude over that of the present NSLS X-ray ring. The low emittance of the high brightness ring's lattice results in a short lifetime, so that a top-off injection mode becomes an operational necessity. Therefore, the NSLS-II injection system must provide, and efficiently inject, an electron beam at a high repetition rate. In this paper, we present our concept of the NSLS-II injection system and discuss the conditions for, and constraints on, its design.

  6. NSLS control system upgrade status

    SciTech Connect

    Smith, J.; Ramamoorthy, S.; Tang, Y.; Flannigan, J.; Sathe, S.; Keane, J.; Krinsky, S.

    1993-07-01

    The NSLS control system initially installed in 1978 has undergone several modifications but the basic system architecture remained relatively unchanged. The need for faster response, increased reliability and better diagnostics made the control system upgrade a priority. Since the NSLS runs continuously, major changes to the control system are difficult. The upgrade plan had to allow continuous incremental changes to the control system without having any detrimental effect on operations. The plan had to provide for immediate improvement in a few key areas, such as data access rates, and be complete in a short time. At present, most accelerator operations utilize the upgraded control system.

  7. Upgrade of NSLS timing system

    SciTech Connect

    Singh, O.; Ramamoorthy, S.; Sheehan, J.; Smith, J.

    1995-05-01

    We report on the progress of the new NSLS timing system. There are three types of requirements for NSLS timing system: clocks, synchronization and trigger circuits. All ring revolution frequency clocks are generated using ECL and high speed TTL logic. The synchronization circuits allows to fill both storage rings with any bunch pattern. The triggers are generated by using commercially available digital delay generators. The delay unit`s outputs are ultrastable, with a resolution of 5 ps, and are programmed by computer via IEEE 488 interface. The block diagrams, description of all major timing components and the present status are provided in this paper.

  8. NSLS-II RF SYSTEMS

    SciTech Connect

    Rose, J.; Gash, W.; Holub, B.; Kawashima, Y.; Ma, H.; Towne, N.; Yeddulla, M.

    2011-03-28

    The NSLS-II is a new third generation light source being constructed at Brookhaven Lab. The storage ring is optimized for low emittance by use of damping wigglers to reduce the emittance to below 1 nm-rad. The RF systems are designed to provide stable beam through tight RF phase and amplitude stability requirements.

  9. Commissioning of NSLS-II

    SciTech Connect

    Willeke, F.

    2015-05-03

    NSLS-II, the new 3rd generation light source at BNL was designed for a brightness of 1022 photons s-1mm-2mrad-2 (0.1%BW)-1. It was constructed between 2009 and 2014. The storage ring was commissioned in April 2014 which was followed by insertion device and beamline commissioning in the fall of 2014. All ambitious design parameters of the facility have already been achieved except for commissioning the full beam intensity of 500mA which requires more RF installation. This paper reports on the results of commissioning.

  10. NSLS-II Beam Diagnostics Overview

    SciTech Connect

    Singh,O.; Alforque, R.; Bacha, B.; Blednykh, A.; Cameron, P.; Cheng, W.; Dalesio, L. B.; Della Penna, A. J.; doom, L.; Fliller, R. P.; Ganetis, G.; Heese, R.; Hseuh, H-C.; Johnson, E. D.; Kosciuk, b. N.; Kramer, S. L.; Krinsky, S.; Mead, J.; Ozaki, S.; Padrazo, D.; Pinayev, I.; Ravindranath, R. V.; Rose, J.; Shaftan, T.; Sharma, S.; Skaritka, J.; Tanabe, T.; Tian, Y.; Willeke, F. J.; Yu, L-H.

    2009-05-04

    A new 3rd generation light source (NSLS-II) is in the early stages of construction at Brookhaven National Laboratory. The NSLS-II facility will provide ultra high brightness and flux with exceptional beam stability. It presents several challenges for diagnostics and instrumentation, related to the extremely small emittance. In this paper, we present an overview of all planned instrumentation systems, results from research and development activities; and then focus on other challenging aspects.

  11. HARMONIC CAVITY PERFORMANCE FOR NSLS-II

    SciTech Connect

    BLEDNYKH, A.; KRINSKY, S.; PODOBEDOV, B.; ROSE, J.; TOWNE, N.; WANG, J.M.

    2005-05-15

    NSLS-II is a 3 GeV ultra-high brightness storage ring planned to succeed the present NSLS rings at BNL. Ultralow emittance combined with short bunch length means that it is critical to minimize the effects of Touschek scattering and coherent instabilities. Improved lifetime and stability can be achieved by including a third-harmonic RF cavity in the baseline design. This paper describes the required harmonic RF parameters and the expected system performance.

  12. Characterization of binary Uranuim oxides by infared spectroscopy

    SciTech Connect

    Allen, G.C.; Holmes, N.R.

    1994-04-01

    In this study, transmission infared spectra were recorded for 15 uranium oxides previously characterized by X-ray diffraction. The infared spectra obtained demonstrated that all the uranium oxides studied could be distinguished, even for the closely similiar structures of UO{sub 2} and U{sub 4}O{sub 9}. The infrared studies of U{sub 4}O{sub 9} near the temperature of the {alpha}-U{sub 4}O{sub 9} to {beta}-U{sub 4}O{sub 9} phase transition showed that an absorption at 670 cm{sup -1} could be related to the ordering of oxygen interstitials in the flourite lattice. A similiar absorption was observed for {beta}-U{sub 3}O{sub 7} but was found to be absent in {alpha}-U{sub 3}O{sub 7}. The local coordination of oxygen/metal clusters in {beta}-U{sub 4}O{sub 9} and {beta}-U{sub 3}O{sub 7} appeared to be similiar. 22 refs., 4 fig., 2 tab.

  13. RGA system for the NSLS

    SciTech Connect

    Schuchman, J.C.; West, L.J.

    1983-01-01

    The National Synchrotron Light Source (NSLS) is a synchrotron radiation source designed to provide photons for simultaneous experiments on a large number of individual beam lines. A residual gas analysis (RGA) system has been designed, and is currently being installed, which would protect the beam lines and the storage rings from contamination from any one offending beam line. The system consists of having separate analyzers, with their associated rf generators, in each beam line and storage ring. The analyzers will be multiplexed back to a central controller. A computer is used for routine monitoring and control. The analyzer chosen was the VG Instruments Model SX-200. Typical mass spectra will be presented along with our specifications for the RGA and our vacuum specifications for operating a typical beam line.

  14. NSLS-II Transport Line Progress

    SciTech Connect

    Fliller R. P.; Wahl, W.; Anderson, A.; Benish, B.; DeBoer, W.; Ganetis, G.; Heese, R.; Hseuh, H.-C.; Hu, J.-P.; Johanson, M.P.; Kosciuk, B.N.; Padrazo, D.; Roy, K.; Shaftan, T.; Singh, O.; Tuozzolo, J.; Wang, G.

    2012-05-20

    The National Synchrotron Light Source II (NSLS-II) is a state-of-the-art 3-GeV third generation light source currently under construction at Brookhaven National Laboratory. The NSLS-II injection system consists of a 200 MeV linac, a 3-GeV booster synchrotron and associated transfer lines. The first part of the Linac to Booster Transport (LBT) line has been installed for linac commissioning. This part includes all components necessary to commission the NSLS-II linac. The second part of this transport line is undergoing installation. Initial results of hardware commissioning will be discussed. The Booster to Storage Ring (BSR) transport line underwent a design review. The first part of the BSR transport line, consisting of all components necessary to commission the booster will be installed in 2012 for booster commissioning. We report on the final design of the BSR line along with the plan to commission the booster.

  15. Ground Motion Studies at NSLS II

    SciTech Connect

    Simos,N.; Fallier, M.; Amick, H.

    2008-06-23

    In this study, an array of vibration measurements at the undisturbed NSLS II site has been performed in order to establish the 'green-field' vibration environment and its spectral characteristics. The interaction of the green-field vibration environment with the NSLS II accelerator structure and the quantification of the storage ring vibration, both in terms of amplitude and spectral content have been assessed through a state-of-the-art wave propagation and scattering analysis. This paper focuses on the wave propagation and scattering aspect as well as on the filtering effects of accelerator structural parameters.

  16. Touschek Lifetime Calculations for NSLS-II

    SciTech Connect

    Nash,B.; Kramer, S.

    2009-05-04

    The Touschek effect limits the lifetime for NSLS-II. The basic mechanism is Coulomb scattering resulting in a longitudinal momentum outside the momentum aperture. The momentum aperture results from a combination of the initial betatron oscillations after the scatter and the non-linear properties determining the resultant stability. We find that higher order multipole errors may reduce the momentum aperture, particularly for scattered particles with energy loss. The resultant drop in Touschek lifetime is minimized, however, due to less scattering in the dispersive regions. We describe these mechanisms, and present calculations for NSLS-II using a realistic lattice model including damping wigglers and engineering tolerances.

  17. NSLS-II RF BEAM POSITION MONITOR

    SciTech Connect

    Vetter, K.; Della Penna, A. J.; DeLong, J.; Kosciuk, B.; Mead, J.; Pinayev, I.; Singh, O.; Tian, Y.; Ha, K.; Portmann, G.; Sebek J.

    2011-03-28

    An internal R&D program has been undertaken at BNL to develop a sub-micron RF Beam Position Monitor (BPM) for the NSLS-II 3rd generation light source that is currently under construction. The BPM R&D program started in August 2009. Successful beam tests were conducted 15 months from the start of the program. The NSLS-II RF BPM has been designed to meet all requirements for the NSLS-II Injection system and Storage Ring. Housing of the RF BPM's in +-0.1 C thermally controlled racks provide sub-micron stabilization without active correction. An active pilot-tone has been incorporated to aid long-term (8hr min) stabilization to 200nm RMS. The development of a sub-micron BPM for the NSLS-II has successfully demonstrated performance and stability. Pilot Tone calibration combiner and RF synthesizer has been implemented and algorithm development is underway. The program is currently on schedule to start production development of 60 Injection BPM's starting in the Fall of 2011. The production of {approx}250 Storage Ring BPM's will overlap the Injection schedule.

  18. DISPERSION TOLERANCE CALCULATION FOR NSLS-II.

    SciTech Connect

    LIN,F.; GUO, W.

    2007-06-25

    In this paper we discuss the effect on the emittance of the residual dispersion in the insertion devices. The dispersion in the straights could be generated by the lattice error, trim dipole, and insertion device. The effect on the emittance is examined, and the dispersion tolerances are given for the NSLS-11.

  19. NSLS-II Radio Frequency Systems

    SciTech Connect

    Rose J.; Gao F.; Goel, A.; Holub, B.; Kulpin, J.; Marques, C.; Yeddulla, M.

    2015-05-03

    The National Synchrotron Light Source II is a 3 GeV X-ray user facility commissioned in 2014. The NSLS-II RF system consists of the master oscillator, digital low level RF controllers, linac, booster and storage ring RF sub-systems, as well as a supporting cryogenic system. Here we will report on RF commissioning and early operation experience of the system.

  20. Optical metrology at the NSLS-II

    SciTech Connect

    Kaznatcheev, K.; Takacs, P. Z.

    2010-12-08

    Rapid progress in synchrotron optics performance places a high demand on optical characterization techniques used to validate surface parameters prior to installation of the X-ray optics. It is now necessary to characterize optical surface figure and slope errors and roughness on meter-long optics over spatial frequencies as short as 0.1 {micro}m The new NSLS-II Optical Metrology Laboratory (OML) includes instruments for measuring: (1) long spatial frequency figure errors with a ZYGO MST Fizeau-type 4* interferometer, capable of 0.1 nm sensitivity, (2) mid spatial frequencies with an upgraded ZYGO NewView 6300 white light interferometric microscope, capable of reaching 0.1 nm accuracy at a lateral resolution of 1 {micro}m, (3) high frequency roughness with an AFM (Nanosurf AG) with linearity better than 0.2% over the 80 {micro}m measurement area and sensitivity approaching 0.01 nm, and (4) slope errors with a long trace profiler currently under development that will be able to reach 50 nrad slope error accuracy. At present, the OML supports the NSLS-II R&D efforts and provides ongoing testing for NSLS optics. Future plans include the construction of a specialized metrology beamline for at-wavelength metrology, radiometry, in situ surface figuring, crystal optics characterization, and instrumentation development.

  1. NSLS-II commissioning and operation

    SciTech Connect

    Wang, G. Shaftan, T.; Bassi, G.; Bengtsson, J.; Blednykh, A.; Blum, E.; Cheng, W.; Choi, J.; Davidsaver, M.; Doom, L.; Fliller, R.; Ganetis, G.; Guo, W.; Hidaka, Y.; Kramer, S.; Li, Y.; Podobedov, B.; Qian, K.; Rose, J.; Seletskiy, S.; and others

    2016-07-27

    The National Synchrotron Light Source II at Brookhaven National Lab is a third-generation synchrotron radiation facility that has been commissioned in 2014. The facility is based on a 3 GeV electron storage ring, which will circulate 500 mA of beam current at 1 nm rad horizontal emittance. The storage ring is 792 meters in circumference and will accommodate more than 60 beamlines in the final built-out. The beamline sources range from insertion-devices located in straight sections, bending magnets or three-pole-wigglers configured in multiple branches. The NSLS-II storage ring commissioning was successfully completed in July 2014 and the facility delivered the first user light on October 23, 2014. Currently the storage ring reached 300 mA beam current and achieved 1 nm rad of horizontal emittance with 3 sets of Damping Wigglers. At this point six NSLS-II project beamlines are routinely taking photons with beam current at 150 mA. This paper reviews the NSLS-II accelerator design and commissioning experience.

  2. Results of the NSLS-II commissioning

    NASA Astrophysics Data System (ADS)

    Wang, Guimei; Shaftan, Timur; Willeke, Ferdinand; NSLS Team, II

    2015-04-01

    The National Synchrotron Light Source II at Brookhaven National Lab is a third-generation synchrotron radiation facility that has been commissioned in 2014. The facility is based on a 3 GeV electron storage ring, which will circulate 500 mA of beam current at 1 nm rad of horizontal emittance. The storage ring is 792 meters in circumference and will accommodate more than 60 beamlines in the final built-out. The beamline sources range from insertion-devices located in straight sections, bending magnets or three-pole-wigglers configured in multiple branches. The linac commissioning activities started in March of 2012 and was accomplished in several weeks. In Dec. 2013 the booster commissioning commenced and reached its goal in February 2014. The commissioning of the NSLS-II storage ring was successfully completed in July 2014, taking about two months in total. The storage ring is now operating at 50 mA with 3 sets of Damping Wigglers resulting in 1 nm rad of horizontal emittance. We delivered the first user light on October 23, 2014. At this point six NSLS-II project beamlines are routinely taking photons since November of 2014. In this presentation I review the NSLS-II accelerator design and our experience with getting ready for the machine start-up. In the following I focus on the commissioning results and present details, issues and advances in reaching the commissioning milestones.

  3. Development of a Tender-Energy Microprobe for Geosciences at NSLS and NSLS-II

    SciTech Connect

    Northrup, Paul A.

    2014-08-30

    This funding is to develop a new Synchrotron user facility for microbeam X-ray absorption spectroscopy (XAS) and quantitative X-ray fluorescence (XRF) imaging, at the National Synchrotron Light Source (NSLS) and NSLS-II. It includes design, purchase of components, and construction of the microprobe endstation and controls. Initial development, commissioning, and application is ongoing at NSLS Beamline X15B, with planned transition in 2014-15 to the NSLS-II TES (Tender-Energy Spatially Resolved X-ray Absorption Spectroscopy) beamline. It is optimized for the “tender” energy range of 1-5 keV, reaching up to 8 keV. Thus it uniquely covers the K absorption edges of critical elements Mg, Al, Si, P, S, Cl, and Ca, and can reach up to Co. A stable, high-flux microbeam focus, user-tunable from ~50 to ~5 microns, has been achieved using two-stage achromatic focusing. Existing beamline optics collimate, monochromate, and macro-focus the X-ray beam to ~1 mm at a secondary source aperture (SSA). Beam from the SSA is then re-focused by a pair of mirrors in KB geometry to the microbeam scale. Size of the microbeam is tunable, at the expense of flux, by adjusting the size of the SSA as a virtual source. The new experimental endstation consists of 1) a sample chamber operable as a radiation enclosure with helium atmosphere to facilitate measurements in this energy range, 2) the KB microfocusing optics, 3) a sample-positioning stage for raster-scanning and positioning the sample, 4) X-ray fluorescence detectors, an existing Ge detector for low-signal sensitivity and a new Si detector for high count rates, 5) an optical camera for viewing samples and locating target locations, 6) beam intensity monitors and diagnostics, and 7) controls and data acquisition system. An important aspect of this project is the added capability for fast, on-the-fly scanning of the monochromator (energy), required for fast XAS and advanced XAS imaging. This instrument will be available for initial PI

  4. NSLS-II Preliminary Design Report

    SciTech Connect

    Dierker, S.

    2007-11-01

    Following the CD0 approval of the National Synchrotron Light Source II (NSLS-II) during August 2005, Brookhaven National Laboratory prepared a conceptual design for a worldclass user facility for scientific research using synchrotron radiation. DOE SC review of the preliminary baseline in December 2006 led to the subsequent CD1 approval (approval of alternative selection and cost range). This report is the documentation of the preliminary design work for the NSLS-II facility. The preliminary design of the Accelerator Systems (Part 1) was developed mostly based of the Conceptual Design Report, except for the Booster design, which was changed from in-storage-ring tunnel configuration to in external- tunnel configuration. The design of beamlines (Part 2) is based on designs developed by engineering firms in accordance with the specification provided by the Project. The conventional facility design (Part 3) is the Title 1 preliminary design by the AE firm that met the NSLS-II requirements. Last and very important, Part 4 documents the ES&H design and considerations related to this preliminary design. The NSLS-II performance goals are motivated by the recognition that major advances in many important technology problems will require scientific breakthroughs in developing new materials with advanced properties. Achieving this will require the development of new tools that will enable the characterization of the atomic and electronic structure, chemical composition, and magnetic properties of materials, at nanoscale resolution. These tools must be nondestructive, to image and characterize buried structures and interfaces, and they must operate in a wide range of temperatures and harsh environments. The NSLS-II facility will provide ultra high brightness and flux and exceptional beam stability. It will also provide advanced insertion devices, optics, detectors, and robotics, and a suite of scientific instruments designed to maximize the scientific output of the facility

  5. ANALYSIS OF NSLS-II TOUSCHEK LIFETIME

    SciTech Connect

    Choi, J.; Kramer, S.L.

    2011-03-28

    As scrapers are adopted for the loss control of NSLS-II storage ring, Touschek lifetime estimations for various cases are required to assure the stable operation. However, to estimate the Touschek lifetime, momentum apertures should be measured all along the ring and, if we want to estimate the lifetime in various situations, it can take extremely long time. Thus, rather than simulating for each case, a semi-analytic methods with the interpolations are used for the measurements of the momentum apertures. In this paper, we described the methods and showed the results. Having enough Touschek lifetime is important for synchrotron light source for the users to perform experiments with stable beams. In NSLS-II, the scrapers will be installed for the loss control. Especially, the horizontal scrapers will be installed where the dispersions are maximum. Therefore, we need to find the proper scraper gap values which do not reduce the lifetime too much for the stable beam operation. To estimate reliable Touschek lifetime, we should measure the momentum apertures at many positions along the ring. For the rough estimation of the Touschek lifetime, the RF momentum acceptance can be used and for a more detailed estimation, the linear approximation of synchrotron oscillation can be used. However, for the strong focussing synchrotrons, like NSLS-II, the linear approximation is not enough to obtain the reliable momentum apertures, and, in general, particle tracking simulations are used. However, for NSLS-II case, we need to track the particle about 400 turns at each point to make it a full synchrotron oscillation period and to obtain the reliable Touschek lifetime we need measure the momentum apertures at several hundred positions at least. Therefore, it can take quite a long time if we want to have the reasonable resolution for the measurements. Furthermore, at the simulation, if we want to measure the aperture inside a element, we should divide the element and this will make the

  6. [FTIR microspectroscopy and its progress in application].

    PubMed

    Li, Xiao-Ting; Zhu, Da-Zhou; Pan, Li-Gang; Ma, Zhi-Hong; Lu, An-Xiang; Wang, Dong; Wang, Ji-Hua

    2011-09-01

    FTIR microspectroscopy technique was born in the mid-nineties. The research on this technique has just began abroad, and this technology has not yet been widely recognized in China. It is a rapid, nondestructive testing technology, has the advantages of microdomain, visualization, high precision and high sensitivity. In the present study, the composition, operational principle and working mode of FTIR microspectroscopy were summarized. The progress in application of FTIR microspectroscopy technique was investigated in some fields, including biomedicine, microbiology, forensic science, materials science, nutrition and feed science and agricultural products. The difficulty of FTIR microspectroscopy research and the prospects of this technique were also discussed.

  7. INSERTION DEVICE UPGRADE PLANS AT THE NSLS.

    SciTech Connect

    TANABE, T.; BLEDNYKH, A.; HARDER, D.; LEHECKA, M.; RAKOWSKY, G.; SKARITKA, J.

    2005-05-16

    This paper describes plans to upgrade insertion devices (IDs) at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory, U.S.A. The aging wiggler (W120) at X25 is being replaced by a 1 m long in-vacuum mini-gap undulator (MGU-X25) optimized for a dedicated macromolecular crystallography program. A new, 1/3 m long, undulator (MGU or SCU-X9), will be installed between a pair of RF cavities at X9, and will serve a new beamline dedicated for small angle x-ray scattering (SAXS). Both IDs will have provision for cryocooling the NdFeB hybrid arrays to 150K to raise the field and K-value and to obtain better spectral coverage. Design issues of the devices and other considerations, especially magnetic measurement at low temperature, will be discussed.

  8. INSERTION DEVICE ACTIVITIES FOR NSLS-II.

    SciTech Connect

    TANABE,T.; HARDER, D.A.; HULBERT, S.; RAKOWSKI, G.; SKARITKA, J.

    2007-06-25

    National Synchrotron Light Source-II (NSLS-II) will be a medium energy storage ring of 3GeV electron beam energy with sub-nm.rad horizontal emittance and top-off capability at 500mA. Damping wigglers will be used not only to reduce the beam emittance but also used as broadband sources for users. Cryo-Permanent Magnet Undulators (CPMUs) are considered for hard X-ray linear device, and permanent magnet based elliptically polarized undulators (EPUs) for variable polarization devices for soft X-ray. 6T superconducting wiggler with minimal fan angle will be installed in the second phase as well as quasi-periodic EPU for VUV and possibly high-temperature superconducting undulator. R&D plans have been established to pursue the performance enhancement of the baseline devices and to design new types of insertion devices. A new insertion device development laboratory will also be established.

  9. Microwave Instability Simulations for NSLS-II

    SciTech Connect

    Blednykh,A.; Krinsky, S.; Nash, B.; Yu, L.

    2009-05-04

    Potential-well distortion and the microwave instability in the NSLS-II storage ring are investigated. The longitudinal wakepotential is calculated as a sum of the contributions due to vacuum chamber components distributed around the ring. An approximation to the wakepotential for a 0.05-mm charge distribution length, much shorter than the 4.5-mm length of the unperturbed circulating bunch, is used as a pseudo-Green's function for beam dynamics simulations. Comparison of particle tracking simulations using the TRANFT code with the Haissinski solution shows good agreement below the instability threshold current. Above threshold two regimes are observed: (1) energy spread and bunch length are time-dependent (saw tooth behavior); (2) both are time-independent.

  10. Growth of Environmental Science at the NSLS

    SciTech Connect

    Northrup,P.; Lanzirotti, A.; Celestian, A.

    2007-01-01

    In the 25 years since the National Synchrotron Light Source (NSLS) began operations, synchrotron 'user facilities' have had a growing impact on research in molecular environmental science (MES). For example, synchrotron-based analytical techniques have allowed researchers to determine the molecular-level speciation of environmentally relevant elements and evaluate their spatial distribution and phase association at very low concentration levels (low parts per million) with micrometer or nanometer resolution [1]. For the environmental scientist, one of the primary advantages of these synchrotron-based techniques is that samples need not be disturbed or destroyed for study; characterization can often be done in-situ in dilute and heterogeneous natural samples with no need for species separation, pre-concentration, or pre-treatment [2]. Liquids, hydrated solids, and biological samples can also often be directly analyzed, which is of fundamental importance in environmental science for understanding the molecular-scale processes that occur at mineral-water interfaces and in understanding how abiotic and biotic processes are involved in the distribution, mobility and ultimate fate of molecular species in the environment.

  11. Shielding Calculations for NSLS-II Beamlines.

    SciTech Connect

    Job,P.K.; Casey, W.R.

    2008-04-13

    Brookhaven National Laboratory is in the process of designing a new Electron Synchrotron for scientific research using synchrotron radiation. This facility, called the 'National Synchrotron Light Source II' (NSLS-II), will provide x-ray radiation of ultra-high brightness and exceptional spatial and energy resolution. It will also provide advanced insertion devices, optics, detectors, and robotics, and a suite of scientific instruments designed to maximize the scientific output of the facility. The project scope includes the design, construction, installation, and commissioning of the following accelerators: a 200 MeV linac, a booster accelerator operating from 200 MeV to 3.0 GeV, the storage ring which stores 500 mA current of electrons at an energy of 3.0 GeV and 56 beamlines for experiments. It is planned to operate the facility primarily in a top-off mode, thereby maintaining the maximum variation in stored beam current to < 1%. Because of the very demanding requirements for beam emittance and synchrotron radiation brilliance, the beam life-time is expected to be quite low, on the order of 2 hours. Each of the 56 beamlines will be unique in terms of the source properties and configuration. The shielding designs for five representative beamlines are discussed in this paper.

  12. BEAM CONTAINMENT SYSTEM FOR NSLS-II

    SciTech Connect

    Kramer, S.L.; Casey, W.; Job, P.K.

    2010-05-23

    The shielding design for the NSLS-II will provide adequate protection for the full injected beam loss in two periods of the ring around the injection point, but the remainder of the ring is shielded for lower losses of {le} 10% full beam. This will require a system to insure that beam losses don't exceed these levels for a period of time that could cause excessive radiation levels outside the shield walls. This beam containment system will measure, provide a level of control and alarm indication of the beam power losses along the beam path from the source (e-gun, linac) thru the injection system and the storage ring. This system will consist of collimators that will provide limits to (and potentially to measure) the beam miss-steering and control the loss points of the charge and monitors that will measure the average beam current losses along the beam path and alarm when this beam power loss exceeds the level set by the shielding specifications. This will require some new ideas in beam loss detection capability and collimation. The initial planning and R&D program will be presented.

  13. Requirements and guidelines for NSLS experimental beam line vacuum systems: Revision A

    SciTech Connect

    Foerster, C.; Halama, H.; Thomlinson, W.

    1986-10-01

    Requirements are provided for NSLS beam line front ends and vacuum interlocks. Guidelines are provided for UHV beam line vacuum systems, including materials, vacuum hardware (pumps, valves, and flanges), acoustic delay lines and beam line fast valves, instrumentation, fabrication and testing, and the NSLS cleaning facility. Also discussed are the design review for experimenters' equipment that would be connected to the NSLS and acceptance tests for any beam line to be connected with the ring vacuum. Also appended are a description of the acoustic delay line as well as the NSLS vacuum standards and NSLS procedures. (LEW)

  14. Optimization of accelerator system performance at the NSLS

    SciTech Connect

    Krinsky, S.

    1994-10-01

    There is an active program of accelerator development at the NSLS aimed at improving reliability, stability and brightness. Work is primarily focused on providing improved performance for the NSLS user community, however, important elements of our work have a generic character and should be of value to other synchrotron radiation facilities. In particular, we have successfully operated a small gap undulator with a full vertical beam aperture of only 3.8 mm, with no degradation of beam lifetime. This provides strong support for the belief that small gap, short period devices will play an important role in the future.

  15. NSLS-II Digital RF Controller Logic and Applications

    SciTech Connect

    Holub, B.; Gao, F.; Kulpin, J.; Marques, C.; Oliva, J.; Rose, J.; Towne, N.

    2015-05-03

    The National Synchrotron Light Source II (NSLS-II) accelerator consists of the Storage Ring, the Booster Ring and Linac along with their associated cavities. Given the number, types and variety of functions of these cavities, we sought to limit the logic development effort by reuse of parameterized code on one hardware platform. Currently there are six controllers installed in the NSLS-II system. There are two in the Storage ring, two in the Booster ring, one in the Linac and one in the Master Oscillator Distribution system.

  16. Status of the NSLS-II Injection System Design

    SciTech Connect

    Shaftan,T.

    2008-06-23

    The NSLS-II is a new ultra-bright 3rd generation 3 GeV light source that will be built at Brookhaven National Laboratory. Its design is well under way. The requirements for the compact injector complex, which will continuously provide 3 GeV electrons for top-off injection into the storage ring, are demanding: high reliability, relatively high charge and low losses. The injector consists of a linear accelerator, a full-energy booster, as well as transport lines, and an injection straight section. In this paper we give an overview of the NSLS-II injector, discuss its status, specifications, and the design challenges.

  17. NSLS-II beamline scattered gas bremsstrahlung radiation shielding calculation

    SciTech Connect

    Popescu, Razvan; Xia, Zhenghua Job, Panakkal; Lee, Wah-Keat

    2016-07-27

    National Synchrotron Light Source II (NSLS-II) is a new state-of-the-art 3rd generation synchrotron. The NSLS-II facility is shielded up to 3 GeV electron beam energy at 500 mA. When the gas bremsstrahlung (GB) from the storage ring is scattered by the beamline components in the first optical enclosure (FOE), the scattered radiation will pose additional radiation hazard (bypassing primary GB collimators and stops) and challenge the FOE shielding. The scattered GB radiation hazard can be mitigated by supplementary shielding or with an exclusion zone downstream of the FOE.

  18. Preliminary Design of Pinhole camera for NSLS-II Project.

    SciTech Connect

    Pinayev,I.; Kosciuk, B.; Singh, O.

    2009-05-04

    The NSLS-II Light Source being built at Brookhaven National Laboratory is expected to provide very small emittances and electron beam sizes. High resolution imaging systems are required in order to provide robust measurements. The pinhole camera will utilize 6-fold magnification with a pinhole placed inside a crotch absorber. The pinhole is protected from high power synchrotron radiation with a filter made of refractory metal. In this paper we provide resolution analyses, heat load calculations, and optimization details for the NSLS-II pinhole camera, including beamline design.

  19. Raman microspectroscopy, surface-enhanced Raman scattering microspectroscopy, and stable-isotope Raman microspectroscopy for biofilm characterization.

    PubMed

    Ivleva, Natalia P; Kubryk, Patrick; Niessner, Reinhard

    2017-07-01

    Biofilms represent the predominant form of microbial life on our planet. These aggregates of microorganisms, which are embedded in a matrix formed by extracellular polymeric substances, may colonize nearly all interfaces. Detailed knowledge of microorganisms enclosed in biofilms as well as of the chemical composition, structure, and functions of the complex biofilm matrix and their changes at different stages of the biofilm formation and under various physical and chemical conditions is relevant in different fields. Important research topics include the development and improvement of antibiotics and medical devices and the optimization of biocides, antifouling strategies, and biological wastewater treatment. Raman microspectroscopy is a capable and nondestructive tool that can provide detailed two-dimensional and three-dimensional chemical information about biofilm constituents with the spatial resolution of an optical microscope and without interference from water. However, the sensitivity of Raman microspectroscopy is rather limited, which hampers the applicability of Raman microspectroscopy especially at low biomass concentrations. Fortunately, the resonance Raman effect as well as surface-enhanced Raman scattering can help to overcome this drawback. Furthermore, the combination of Raman microspectroscopy with other microscopic techniques, mass spectrometry techniques, or particularly with stable-isotope techniques can provide comprehensive information on monospecies and multispecies biofilms. Here, an overview of different Raman microspectroscopic techniques, including resonance Raman microspectroscopy and surface-enhanced Raman scattering microspectroscopy, for in situ detection, visualization, identification, and chemical characterization of biofilms is given, and the main feasibilities and limitations of these techniques in biofilm research are presented. Future possibilities of and challenges for Raman microspectroscopy alone and in combination with other

  20. Microspectroscopy At Beamline 73 MAX-lab

    SciTech Connect

    Engdahl, Anders

    2010-02-03

    Presentation of some projects at the infrared microspectroscopy experimental station at beamline 73 MAX-lab. Among the subjects are found identification of organic residues in fossil material and examination of the chemistry in an old oak wood wreck.

  1. Capabilities and Limitations of Infrared Reflectance Microspectroscopy

    NASA Technical Reports Server (NTRS)

    Klima, R. L.; Pieters, C. M.

    2005-01-01

    Technological improvements in IR microspectroscopy have made it an increasingly appealing tool for planetary mineralogy. Microspectroscopy presents the prospect of examining small samples nondestructively and acquiring spectra that can be related to remote sensing observations. However, complications are introduced as a target beam size is reduced, and it is critical that limitations are understood. We present the results of a series of well constrained spectroscopic measurements, linking microspectroscopic data to traditionally collected reflectance spectra and petrologic information for the same rock.

  2. CONCEPTUAL DESIGN OF THE NSLS-II INJECTION SYSTEM.

    SciTech Connect

    SHAFTAN,T.; ROSE, T.; PINAYEV, I.; HEESE, R.; BENGTSSON, J.; SKARITKA, J.; MENG, W.; OZAKI, S.; MEIER, R.; STELMACH, C.; LITVINENKO, V.; PJEROV, S.; SHARMA, S.; GANETIS, G.; HSEUH, H.C.; JOHNSON, E.D.; TSOUPAS, N.; GUO, W.; BEEBE-WANG, J.; LUCCIO, A.U.; YU, L.H.; RAPARIA, D.; WANG, D.

    2007-06-25

    We present the conceptual design of the NSLS-II injection system [1,2]. The injection system consists of a low-energy linac, booster and transport lines. We review two different injection system configurations; a booster located in the storage ring tunnel and a booster housed in a separate building. We briefly discuss main parameters and layout of the injection system components.

  3. Digital signal array processor for NSLS booster power supply upgrade

    SciTech Connect

    Olsen, R.; Dabrowski, J.; Murray, J.

    1993-07-01

    The booster at the NSLS is being upgraded from 0.75 to 2 pulses per second. To accomplish this, new power supplied for the dipole, quadrupole, and sextupole have been installed. This paper will outline the design and function of the digital signal processor used as the primary control element in the power supply control system.

  4. Rogue Mode Shileding in NSLS-II Multipole Vacuum Chambers

    SciTech Connect

    Ferreira, M.; Blednykh, A.; Bacha, B.; Borrelli, A.; Hseuh, H.-C.; Kosciuk, B.; Krinsky, S.; Singh, O.; Vetter, K.

    2011-03-28

    Modes with transverse electric field (TE-modes) in the NSLS-II multipole vacuum chamber can be generated at frequencies above 450MHz due to its geometric dimensions. Since the NSLS-II BPM system monitors signals within 10 MHz band at RF frequency of 500 MHz, frequencies of higher-order modes (HOM) can be generated within the transmission band of the band pass filter. In order to avoid systematic errors in the NSLS-II BPM system, we introduced frequency shift of HOMs by using RF metal shielding located in the antechamber slot. We demonstrated numerical modeling and experimental studies of the spurious TE modes in the NSLS-II vacuum chambers with antechamber slot. Calculated frequencies of TE-modes in considered chambers with and without RF shielding were verified experimentally. Flexible BeCu RF shielding inside each chamber at proper location shifts frequencies of H{sub 10p}-modes above {approx}900MHz, except chambers S6 odd and even. These chambers need special attention because of synchrotron radiation from downstream magnets. S6 odd multipole vacuum chamber needs to be measured and the RF shielding length has to be optimized. RF shielding looks adequate for baseline design. Fifty percent of open space provides adequate pumping speed.

  5. Design of NSLS-II High Order Multipole Correctors

    SciTech Connect

    Rehak,M.; Danby, G.; Bengtsson, Jo; Jackson, J.; Skaritka, J.; Spataro, C.

    2009-05-04

    Feasibility studies for two families of corrector magnets for NSLS-II are presented. The first family of magnets are generalizations of figure eight quadrupoles using rotationally symmetric breaks in the return yoke to fit in available space. Properties specific to figure eight magnet are identified. The second type of magnet is a combined sextupole/dipole trim.

  6. Another First at NSLS-II Construction Site

    ScienceCinema

    None

    2016-07-12

    Workers at the NSLS-II ring building construction site recently completed the first complicated concrete pour for the approximately 19-ft.-tall walls of the Utility Tunnel. The continuous pour was the first of its kind, as previous pours have been for foo

  7. Another First at NSLS-II Construction Site

    SciTech Connect

    2009-08-21

    Workers at the NSLS-II ring building construction site recently completed the first complicated concrete pour for the approximately 19-ft.-tall walls of the Utility Tunnel. The continuous pour was the first of its kind, as previous pours have been for foo

  8. Control system for NSLS booster power supply upgrade II

    SciTech Connect

    Olsen, R.; Dabrowski, J.; Murray, J.

    1993-07-01

    The booster at the NSLS is being upgraded from 0.75 to 2 pulses per second by means of the installation of new dipole, quadrupole, and sextupole power supplies. Here the authors outline the design of the power supply control system.

  9. First Concrete Poured for NSLS-II Ring Building

    SciTech Connect

    2009-07-20

    The first bits of the National Synchrotron Light Source II (NSLS-II) ring building are now taking shape after the concrete-pouring process for the new, world-class facility began on Monday, July 20. Once complete, the 400,000 square-foot building will house the accelerator ring, the largest component of the machine.

  10. Energy deposition and non-equilibrium infared radiation of energetic auroral electrons

    NASA Astrophysics Data System (ADS)

    Wu, Yadong; Gao, Bo; Zhu, Guangsheng; Li, Ziguang

    2016-07-01

    Infrared radiation caused by energetic auroral electrons plays an important role in the thermospheric hear budget, and may be seen as background by infrared surveillance sensors. The auroral electron deposition leads to the ionization, excitation, and dissociation of neutral species(N2,O2,and O), and initiates a series of chemical reaction in the upper atmosphere, finally causes the optical emission of infared excited emitters. In this study, the whole progress from the initial auroral electrons energy deposition to the final infrared emissions has been modeled, which including space plasma, atmospheric physical chemistry, and radiative transfer. The initial atmosphere parameters before auroral disturbing are given by MSIS00 model. The primary electron flux at the top of atmosphere is given by a statistical fitting with the sum of three distribution terms, a power law, a Maxwellian and a Guassian. A semi-emprical model is used in the calculation of energy depositon of single primary electron. The total integral ion pairs production rate is obtained after combining with the initial primary electron flux. The production rate and flux of secondary electrons are modeled with a continuous slow down approximation, using different excitation, ionization, dissociation cross sections of N2, O2, and O to electrons. The photochemical reactions with auroral disturbance is analysed, and its calculation model is established. A "three-step" calculation method is created to obtain number densities of eleven species in the hight between 90-160 km, which containing N2+, O2+, O+, O2+(a4Π), O+(2D), O+(2P), N2(A3Σ), N(2D), N(4S), NO+, and N+. Number densities of different vibraional levels of NO and NO+ are got with steady state assumption, considering 1-12 vibrational levels of NO and 1-14 vibrational levels of NO+. The infared emissions and the spectral lines of the two radiating bodies are calculated with a fuzzy model of spectral band.

  11. PHILOSOPHY FOR NSLS-II DESIGN WITH SUB-NANOMETER HORIZONTAL EMITTANCE.

    SciTech Connect

    OZAKI,S.; BENGTSSON, J.; KRAMER, S.L.; KRINSKY, S.; LITVINENKO, V.N.

    2007-06-25

    NSLS-II at Brookhaven National Laboratory is a new third-generation storage ring light source, whose construction is on the verge of being approved by DOE. When completed, NSLS-II with its ability to provide users with a wide range of spectrum, ranging from IR to ultra-high brightness hard x-ray beams will replace the existing two (20+ years old) NSLS light sources. While presenting an overview of the NSLS-II accelerator system, this paper focuses on the strategy and development of a novel <1 nm emittance light source.

  12. Infrared microspectroscopy with synchrotron radiation

    SciTech Connect

    Carr, G.L.; Williams, G.P.

    1997-09-01

    Infrared microspectroscopy with a high brightness synchrotron source can achieve a spatial resolution approaching the diffraction limit. However, in order to realize this intrinsic source brightness at the specimen location, some care must be taken in designing the optical system. Also, when operating in diffraction limited conditions, the effective spatial resolution is no longer controlled by the apertures typically used for a conventional (geometrically defined) measurement. Instead, the spatial resolution depends on the wavelength of light and the effective apertures of the microscope`s Schwarzchild objectives. The authors have modeled the optical system from the synchrotron source up to the sample location and determined the diffraction-limited spatial distribution of light. Effects due to the dependence of the synchrotron source`s numerical aperture on wavelength, as well as the difference between transmission and reflection measurement modes, are also addressed. Lastly, they examine the benefits (when using a high brightness source) of an extrinsic germanium photoconductive detector with cone optics as a replacement for the standard MCT detector.

  13. Impedance Calculations for the NSLS-II Storage Rings

    SciTech Connect

    Blednykh,A.; Ferreira, M.; Krinsky, S.

    2009-05-04

    Impedance of two vacuum chamber components, Bellows and BPM, is considered in some detail. In order to avoid generation of Higher-Order Modes (HOM's) in the NSLS-II bellows, we designed a new low-impedance RF shielding consisting of 6 wide and 2 narrow metal plates without opening slots between them. The short-range wakepotential has been optimized taking into account vertical offset of RF fingers from their nominal position. The results were compared with data of bellows designed at other laboratories. Narrow-band impedance of the BPM Button has been studied. TE-modes in the BPM button were suppressed by a factor of 8 by modification of existing housings. Two new types of housings are shown. The total impedance of the NSLS-II storage ring is discussed in terms of the loss factor and the vertical kick factor for a 3mm-Gaussian bunch.

  14. DESIGN OF BEAM TRANSFER LINES FOR THE NSLS II

    SciTech Connect

    TSOUPAS,N.; ROSE, J.; PINAYEV, I.; SHAFTAN, T.; STELMACH, C.

    2007-06-25

    The NSLS-II light source which is a proposed facility to be built at Brookhaven National Laboratory utilizes two synchrotron accelerator rings: the booster and the Storage ring (SR). Designing the NSLS-11 injector we considered two options for the booster layout, where the rings either (a) share the same tunnel, but placed at different horizontal planes or (b) booster is located in a separate building. The booster which accepts beam from the linac, accelerates the electron beam to an energy of 3.0 GeV and the beam is extracted to the Booster to Storage Ring (BtS) transport line which transports the beam and injects it into the SR ring. The design procedure for each of the two options of the BtS line and other details about the optics and the magnetic elements of the line are presented in this paper.

  15. DEGRADATION OF MAGNET EPOXY AT NSLS X-RAY RING.

    SciTech Connect

    HU,J.P.; ZHONG,Z.; HAAS,E.; HULBERT,S.; HUBBARD,R.

    2004-05-24

    Epoxy resin degradation was analyzed for NSLS X-ring magnets after two decades of 2.58-2.8 GeV continuous electron-beam operation, based on results obtained from thermoluminescent dosimeters irradiated along the NSLS ring and epoxy samples irradiated at the beamline target location. A Monte Carlo-based particle transport code, MCNP, was utilized to verify the dose from synchrotron radiation distributed along the axial- and transverse-direction in a ring model, which simulates the geometry of a ring quadrupole magnet and its central vacuum chamber downstream of the bending-magnet photon ports. The actual life expectancy of thoroughly vacuum baked-and-cured epoxy resin was estimated from radiation tests on similar polymeric materials using a radiation source developed for electrical insulation and mechanical structure studies.

  16. Beam Loss Monitors in the NSLS Storage Rings

    SciTech Connect

    Kramer,S.L.; Fedurin, M.

    2009-05-04

    Beam loss monitors (BLM) have been used for more than two decades in the VUV ring at the NSLS. These have proved useful for optimizing injection and operation of the ring. Recently similar monitors have been installed in the X-ray ring and are being used to better understand injection, as well as operation of the ring. These units have been compared with the Bergoz BLMs, which have been mostly useful for understanding operating beam losses.

  17. NSLS-II BPM System Protection from Rogue Mode Coupling

    SciTech Connect

    Blednykh, A.; Bach, B.; Borrelli, A.; Ferreira, M.; Hseuh, H.-C.; Hetzel, C.; Kosciuk, B.; Krinsky, S.; Singh, O.; Vetter, K.

    2011-03-28

    Rogue mode RF shielding has been successfully designed and implemented into the production multipole vacuum chambers. In order to avoid systematic errors in the NSLS-II BPM system we introduced frequency shift of HOM's by using RF metal shielding located in the antechamber slot of each multipole vacuum chamber. To satisfy the pumping requirement the face of the shielding has been perforated with roughly 50 percent transparency. It stays clear of synchrotron radiation in each chamber.

  18. Accelerator Physics Challenges for the NSLS-II Project

    SciTech Connect

    Krinsky,S.

    2009-05-04

    The NSLS-II is an ultra-bright synchrotron light source based upon a 3-GeV storage ring with a 30-cell (15 super-period) double-bend-achromat lattice with damping wigglers used to lower the emittance below 1 nm. In this paper, we discuss the accelerator physics challenges for the design including: optimization of dynamic aperture; estimation of Touschek lifetime; achievement of required orbit stability; and analysis of ring impedance and collective effects.

  19. PERFORMANCE OF THE DIAGNOSTICS FOR NSLS-II LINAC COMMISSIONING

    SciTech Connect

    Fliller III, R.; Padrazo, D.; Wang, G.M.; Heese, R.; Hseuh H.-C.; Johanson, M.; Kosciuk, B.N.; Pinayev, I.; Rose, J.; Shaftan, T.; Singh, O.

    2011-03-28

    The National Synchrotron Light Source II (NSLS-II) is a state of the art 3-GeV third generation light source currently under construction at Brookhaven National Laboratory. The NSLS-II injection system consists of a 200 MeV linac, a 3-GeV booster synchrotron and associated transfer lines. The transfer lines not only provide a means to deliver the beam from one machine to another, they also provide a suite of diagnostics and utilities to measure the properties of the beam to be delivered. In this paper we discuss the suite of diagnostics that will be used to commission the NSLS-II linac and measure the beam properties. The linac to booster transfer line can measure the linac emittance with a three screens measurement or a quadrupole scan. Energy and energy spread are measured in a dispersive section. Total charge and charge uniformity are measured with wall current monitors in the linac and transformers in the transfer line. We show that the performance of the diagnostics in the transfer line will be sufficient to ensure the linac meets its specifications and provides a means of trouble shooting and studying the linac in future operation.

  20. Design and Measurement of the NSLS II Correctors

    SciTech Connect

    Spataro, C.; Danby, G.; Jackson, J.W.; Jain, A.K.; Rehak, M.; Singh, O. Skaritka, J.

    2009-05-04

    The National Synchrotron Light Source II (NSLS-II) under construction at Brookhaven National Laboratory will be a new state-of-the-art 3 Gev electron storage ring designed to deliver world-leading intensity and brightness, and will produce x-rays more than 10,000 times brighter than the current NSLS at Brookhaven. The 792-meter circumference storage ring is comprised of approximately 1000 magnetic elements, 300 of which are discrete corrector magnets. The three variants are: 120 of the 100 mm aperture correctors, 60 of the 156 mm aperture correctors, and 90 of the air core correctors.[1] The 100 mm and 156 mm horizontal and vertical dipole correctors come in two varieties: with and without a DC skew quad corrector. The air core is strictly an AC horizontal and vertical dipole corrector. The specifications are listed. Discrete corrector magnets are used for the 230 horizontal and vertical steering magnets in the NSLS-II storage ring. A unique design incorporates both dipole and skew quad correctors for (DC) steering in the same magnet. Separate AC (orbit feedback) correctors have also been designed. Comparison with alternate designs are presented as well as prototype measurements.

  1. Design of the NSLS-II Top-Off Safety System

    SciTech Connect

    Fliller, III R.; Doom, L.; Ganetis, G.; Hetzel, C.; Job, P. K.; Li, Y.; Shaftan, T.; Sharma, S.; Singh, O.; Wang, G. M.; Xia, Z.

    2015-05-03

    The NSLS-II accelerators finished commissioning in the fall of 2014, with beamline commissioning underway. Part of the design for the NSLS-II is to operate in top off mode. The Top Off Safety System (TOSS) is presently being installed. In this report we discuss the Top Off Safety System design and implementation, along with the necessary tracking results and radiological calculations.

  2. Applications of hierarchical cluster analysis (CLA) and principal component analysis (PCA) in feed structure and feed molecular chemistry research, using synchrotron-based Fourier transform infrared (FTIR) microspectroscopy.

    PubMed

    Yu, Peiqiang

    2005-09-07

    Synchrotron technology based Fourier transform infrared microspectroscopy (S-FTIR) is a recently emerging bioanalytical microprobe capable of exploring the molecular chemistry within microstructures of feed tissues at a cellular or subcellular level. To date there has been very little application of hierarchical cluster analysis (CLA) and principal component analysis (PCA) to the study of feed inherent microstructures and feed molecular chemistry between feeds and/or between different structures within a feed, in relation to feed quality and nutrient availability using S-FTIR. In this paper, multivariate statistical methods--CLA and PCA--were used to analyze synchrotron-based FTIR individual spectra obtained from feed inherent microstructures within intact tissues by using the S-FTIR as a novel approach. The S-FTIR spectral data of three feed inherent structures (strucutre 1, feed pericarp; structure 2, feed aleurone; structure 3, feed endosperm) and different varieties of feeds within cellular dimensions were collected at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory (BNL), U.S. Department of Energy (NSLS-BNL, New York). Both PCA and CLA methods gave satisfactory analytical results and are conclusive in showing that they can discriminate and classify inherent structures and molecular chemistry between and among the feed tissues. They also can be used to identify whether differences exist between the varieties. These statistical analyses place synchrotron-based FTIR microspectroscopy at the forefront of those new potential techniques that could be used in rapid, nondestructive, and noninvasive screening of feed intrinsic microstructures and feed molecular chemistry in relation to the quality and nutritive value of feeds.

  3. DESIGN OF VISIBLE DIAGNOSTIC BEAMLINE FOR NSLS2 STORAGE RING

    SciTech Connect

    Cheng, W.; Fernandes, H.; Hseuh, H.; Kosciuk, B.; Krinsky, S.; Singh, O.

    2011-03-28

    A visible synchrotron light monitor (SLM) beam line has been designed at the NSLS2 storage ring, using the bending magnet radiation. A retractable thin absorber will be placed in front of the first mirror to block the central x-rays. The first mirror will reflect the visible light through a vacuum window. The light is guided by three 6-inch diameter mirrors into the experiment hutch. In this paper, we will describe design work on various optical components in the beamline. The ultra high brightness NSLS-II storage ring is under construction at Brookhaven National Laboratory. It will have 3GeV, 500mA electron beam circulating in the 792m ring, with very low emittance (0.9nm.rad horizontal and 8pm.rad vertical). The ring is composed of 30 DBA cells with 15 fold symmetry. Three damping wigglers will be installed in long straight sections 8, 18 and 28 to lower the emittance. While electrons pass through the bending magnet, synchrotron radiation will be generated covering a wide spectrum. There are other insertion devices in the storage ring which will generate shorter wavelength radiation as well. Synchrotron radiation has been widely used as diagnostic tool to measure the transverse and longitudinal profile. Three synchrotron light beam lines dedicated for diagnostics are under design and construction for the NSLS-II storage ring: two x-ray beam lines (pinhole and CRL) with the source points from Cell 22 BM{_}A (first bending in the DBA cell) and Cell22 three-pole wiggler; the third beam line is using visible part of radiation from Cell 30 BM{_}B (second bending magnet from the cell). Our paper focuses on the design of the visible beam line - SLM.

  4. The Latest Status of NSLS-II Insertion Devices

    NASA Astrophysics Data System (ADS)

    Tanabe, Toshi; Kitegi, Charles; He, Ping; Musardo, Marco; Rank, Oleg Chubar James; Cappadoro, Peter; Fernandes, Huston; Harder, David; Corwin, Todd

    2014-03-01

    The National Synchrotron Light Source-II (NSLS-II) project is now in the final stage of construction. The Linac, the Booster synchrotron, and the Storage Ring magnets girder assemblies have been installed. The first damping wiggler has been delivered and its field characteristics are carefully measured. A Three Pole Wiggler (3PW) and Apple-II type elliptically polarizing undulators (EPUs) have been fabricated by the vendors. Two 3.0m long in-vacuum undulators (IVUs) and one 1.5m long IVU are almost complete and waiting for factory acceptance tests. One 3.0m long IVU for Inelastic X-ray Scattering beamline is in fabrication by a different vendor. Recently two 2.8m long IVUs for long straight sections (LSSs) have been added to the project for "future beamlines". In addition, two 1.5m long IVUs and one 2.8m long IVU for LSSs have been procured for Advanced Beamlines for Biological Investigations with X-rays (ABBIX) project funded by National Institure of Health (NIH). Further, two 3.5m long EPUs for LSSs are being designed for NSLS-II Experimental Tools (NEXT) -Major Item of Equipment (MIE) project. To succeed these conventional IVUs, PrFeB based cryo-permanent magnet undulator (CPMU) is considered as next generation device of hard X-ray sources. An In-Vacuum Magnetic Measurement System (IVMMS) for cold in-situ Hall probe mapping of CPMUs up to 1.5m in length has been developed. Summary of the current status of each project and future plans for the NSLS-II ring will be discussed.

  5. Kinematic mounting systems for NSLS beamlines and experiments

    SciTech Connect

    Oversluizen, T.; Stoeber, W.; Johnson, E.D.

    1991-01-01

    Methods for kinematically mounting equipment are well established, but applications at synchrotron radiation facilities are subject to constraints not always encountered in more traditional laboratory settings. Independent position adjustment of beamline components can have significant benefits in terms of minimizing time spent aligning, and maximizing time spent acquiring data. In this paper, we use examples taken from beamlines at the NSLS to demonstrate approaches for optimization of the reproducibility, stability, excursion, and set-up time for various situations. From our experience, we extract general principles which we hope will be useful for workers at other synchrotron radiation facilities. 7 refs., 4 figs.

  6. Macromolecular crystallography beamline X25 at the NSLS.

    PubMed

    Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L; Dvorak, Joseph; Flaks, Leon; Lamarra, Steven; Myers, Stuart F; Orville, Allen M; Robinson, Howard H; Roessler, Christian G; Schneider, Dieter K; Shea-McCarthy, Grace; Skinner, John M; Skinner, Michael; Soares, Alexei S; Sweet, Robert M; Berman, Lonny E

    2014-05-01

    Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.

  7. MECHANICAL DESIGN OF NSLS MINI - GAP UNDULATOR (MGU)

    SciTech Connect

    LYNCH,D.; RAKOWSKY,G.

    2002-09-05

    The mechanical design considerations are discussed with respect to the currently installed X-13 and future X-29 MGU. Comparisons to the previous 2 generations of variable small-gap undulator evolution in the NSLS X-ray ring are made and design improvements noted. The design requirements and mechanical difficulties for holding, positioning and driving the magnetic arrays are explored. Structural, thermal and electrical considerations which influenced the design are then analyzed. The mechanical performance of the MGU currently installed at X-13 is examined and future installations and enhancements are presented.

  8. Macromolecular crystallography beamline X25 at the NSLS

    PubMed Central

    Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E.

    2014-01-01

    Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community. PMID:24763654

  9. SIMULATIONS OF TRANSVERSE STACKING IN THE NSLS-II BOOSTER

    SciTech Connect

    Fliller III, R.; Shaftan, T.

    2011-03-28

    The NSLS-II injection system consists of a 200 MeV linac and a 3 GeV booster. The linac needs to deliver 15 nC in 80 - 150 bunches to the booster every minute to achieve current stability goals in the storage ring. This is a very stringent requirement that has not been demonstrated at an operating light source. We have developed a scheme to transversely stack two bunch trains in the NSLS-II booster in order to alleviate the charge requirements on the linac. This scheme has been outlined previously. In this paper we show particle tracking simulations of the tracking scheme. We show simulations of the booster ramp with a stacked beam for a variety of lattice errors and injected beam parameters. In all cases the performance of the proposed stacking method is sufficient to reduce the required charge from the linac. For this reason the injection system of the NSLS-II booster is being designed to include this feature. The NSLS-II injection system consists of a 200 MeV linac and a 3 GeV booster. The injectors must provide 7.5nC in bunch trains 80-150 bunches long every minute for top off operation of the storage ring. Top off then requires that the linac deliver 15nC of charge once losses in the injector chain are taken into consideration. This is a very stringent requirement that has not been demonstrated at an operating light source. For this reason we have developed a method to transversely stack two bunch trains in the booster while maintaining the charge transport efficiency. This stacking scheme has been discussed previously. In this paper we show the simulations of the booster ramp with a single bunch train in the booster. Then we give a brief overview of the stacking scheme. Following, we show the results of stacking two bunch trains in the booster with varying beam emittances and train separations. The behavior of the beam through the ramp is examined showing that it is possible to stack two bunch trains in the booster.

  10. Status of NSLS-II Storage Ring Vacuum Systems

    SciTech Connect

    Doom,L.; Hseuh,H.; Ferreira, M.; Longo, C.; Ravindranath, V.; Settepani, P.; Sharma, S.; Wilson, K.

    2009-05-04

    National Synchrotron Light Source II (NSLS-II), being constructed at Brookhaven National Laboratory, is a 3-GeV, high-flux and high- brightness synchrotron radiation facility with a nominal current of 500 mA. The storage ring vacuum system will have extruded aluminium chambers with ante-chamber for photon fans and distributed NEG strip pumping. Discrete photon absorbers will be used to intercept the un-used bending magnet radiation. In-situ bakeout will be implemented to achieve fast conditioning during initial commissioning and after interventions.

  11. INVESTIGATION OF COHERENT EMISSION FROM THE NSLS VUV RING.

    SciTech Connect

    CARR,G.L.; KRAMER,S.L.; MURPHY,J.B.; LAVEIGNE,J.; LOBO,R.P.S.; REITZE,D.H.; TANNER,D.B.

    1999-03-01

    Bursts of coherent radiation are observed from the NSLS VUV ring near a wavelength of 7 mm. The bursts occur when the electron beam current (I) exceeds a threshold value (I{sub th}), which itself varies with ring operating conditions. Beyond threshold, the average intensity of the emission is found to increase as (I-I{sub th}){sup 2}. With other parameters held nearly constant, the threshold current value is found to increase quadratically with synchrotron frequency, indicating a linear dependence on momentum compaction. It is believed that the coherent emission is a consequence of micro-bunching of the electron beam due to the microwave instability.

  12. MULTIOBJECTIVE DYNAMIC APERTURE OPTIMIZATION AT NSLS-II

    SciTech Connect

    Yang, L.; Li, Y.; Guo, W.; Krinsky, S.

    2011-03-28

    In this paper we present a multiobjective approach to the dynamic aperture (DA) optimization. Taking the NSLS-II lattice as an example, we have used both sextupoles and quadrupoles as tuning variables to optimize both on-momentum and off-momentum DA. The geometric and chromatic sextupoles are used for nonlinear properties while the tunes are independently varied by quadrupoles. The dispersion and emittance are fixed during tunes variation. The algorithms, procedures, performances and results of our optimization of DA will be discussed and they are found to be robust, general and easy to apply to similar problems.

  13. Materials research and beam line operation utilizing NSLS. Progress report

    SciTech Connect

    Liedl, G.L.

    1993-06-01

    MATRIX, a participating research team of Midwest x-ray scattering specialists, continues to operate beam line X-18A at NSLS. Operations of this line now provides state-of-the-art capabilities to a wide range of people in the Materials Science and Engineering research community. Improvements of the beam line continue to be a focus of MATRIX. Throughout this past year the emphasis has been shifting towards improvement in ``user friendly`` aspects. Simplified control operations and a shift to single-user personal computer has been a major part of the effort. Over the past year all 232 operational days were fully utilized. Beam line tests coupled with MATRIX members combined to use 284 days. General user demand for use of the beam line continues to be strong and four groups were provided 48 operating days. Research production has been growing as NSLS and the beam line become a more stable type of operation. For 1992 the MATRIX group published six articles. To date, for 1993 the same group has published, submitted, or has in preparation nine articles. Recent research milestones include: the first quantitative structural information on the as-quenched and early stages of decomposition of supersaturated Al-Li alloys; the first quantitative diffuse scattering measurements on a complex system (Co substitute for Cu YBCO superconductor); demonstration of capabilities of a new UHV surface diffraction chamber with in-situ characterization and temperature control (30-1300K); feasibility of phasing structure factors in a quasicrystal using multiple Bragg scattering.

  14. Insertion Devices for NSLS-II Baseline and Future

    SciTech Connect

    Tanabe,T.

    2008-06-23

    NSLS-II is going to employ Damping Wigglers (DWs) not only for emittance reduction but also as broad band hard X-ray source. In-Vacuum Undulators (IVUs) with the minimum RMS phase error (< 2 degree) and possible cryo-capability are planned for X-ray planar device. Elliptically Polarized Undulators (EPUs) are envisioned for polarization controls. Due to the lack of hard X-ray flux from weak dipole magnet field (0.4 Tesla), three pole wigglers (3PWs) of the peak field over 1 Tesla will be mainly used by NSLS bending magnet beam line users. Magnetic designs and kick maps for dynamic aperture surveys were created using the latest version of Radia [1] for Mathematica 6 which we supported the development. There are other devices planned for the later stage of the project, such as quasi-periodic EPU, superconducting wiggler/undulator, and Cryo-Permanent Magnet Undulator (CPMU) with Praseodymium Iron Boron (PrFeB) magnets and textured Dysprosium poles. For R&D, Hybrid PrFeB arrays were planned to be assembled and field-measured at room temperature, liquid nitrogen and liquid helium temperature using our vertical test facility. We have also developed a specialized power supply for pulsed wire measurement.

  15. NSLS-II injector commissioning and initial operation

    SciTech Connect

    Bacha, B.; Blum, E.; Bassi, B.; Bengtsson, J.; Blednykh, A.; Buda, S.; Cheng, W.; Choi, J.; Cuppolo, J.; D Alsace, R.; Davidsaver, M.; DeLong, J.; Doom, L.; Durfee, d.; fliller, R.; Fulkerson, M.; Ganetis, G.; Gao, F.; Gardner, C.; Guo, W.; Heese, R.; Hidaka, Y.; Hu, Y.; Johanson, M.; Kosciuk, B.; Kowalski, S.; Dramer, S.; Krinsky, S.; Li, Y.; Louie, W.; Maggipinto, M.; Marino, P.; Mead, J.; Oliva, G.; Padrazo, D.; Pedersen, K.; Podobedov, B.; Rainer, R.; Rose, J.; Santana, M.; Seletskiy, S.; Shaftan, T.; Singh, O.; Singh, P.; Smalyuk, V.; Smith, R.; Summers, T.; Tagger, J.; Tian, Y.; Wahl, W.; Wang, G.; Weiner, G.; Willeke, F.; Yang, L.; Yang, X.; Zeitler, E.; Zitvogel, E.; Zuhoski, P.

    2015-05-03

    The injector for the National Synchrotron Light Source II (NSLS-II) storage ring consists of a 3 GeV booster synchrotron and a 200 MeV S-band linac. The linac was designed to produce either a single bunch with a charge of 0.5 nC of electrons or a train of bunches up to 300 ns long containing a total charge of 15 nC. The booster was designed to accelerate up to 15 nC each cycle in a train of bunches up to 300 ns long. Linac commissioning was completed in April 2012. Booster commissioning was started in November 2013 and completed in March 2014. All of the significant design goals were satisfied including beam emittance, energy spread, and transport efficiency. While the maximum booster charge accelerated was only 10 nC, this has proven to be more than sufficient for storage ring commissioning and operation. The injector has operated reliably during storage ring operation since then. Results will be presented showing measurements of linac and booster operating parameters achieved during commissioning and initial operation. Operating experience and reliability during the first year of NSLS-II operation will be discussed.

  16. NSLS transvenous coronary angiography beamline upgrade and advanced technology initiatives

    SciTech Connect

    Gmuer, N.F.; Chapman, D.; Thomlinson, W.; Thompson, A.C.; Lavender, W.M.; Scalia, K.; Malloy, N.; Mangano, J.; Jacob, J.

    1994-11-01

    Since October 1990, the coronary anatomies of a total of 16 patients (male and female) have been imaged at the National Synchrotron Light Source (NSLS) as part of the Dual Energy Digital Subtraction Transvenous Coronary Angiography research program. This program takes place in the Synchrotron Medical Research Facility (SMERF) on the X17B2 wiggler beamline. Encouraged by the success of the initial patient images, the NSLS has recently embarked on an ambitious upgrade effort. This effort covers all aspects of the X17B2 beamline and includes improved radiation shielding, a Laue monochromator assembly, a computer-controlled 5 motion patient scanning chair assembly, a fast low-noise image acquisition system, and a modularized patient safety system. These improvements will allow major advances in imaging patients based on ECG signal gating and multiple view imaging. Two advanced technology initiatives are underway with industrial collaborators. One will develop real-time image acquisition and display of the subtracted digital images. The second will develop a compact x-ray source for medical imaging. The source will be a linear electron accelerator creating characteristic radiation line emissions.

  17. NSLS transvenous coronary angiography beamline upgrade and advanced technology initiatives

    SciTech Connect

    Gmuer, N.F.; Chapman, D.; Thomlinson, W. ); Thompson, A.C. ); Lavender, W.M. ); Scalia, K.; Malloy, N. ); Mangano, J.; Jacob, J. )

    1995-02-01

    Since October 1990, the coronary anatomies of a total of 16 patients (male and female) have been imaged at the National Synchrotron Light Source (NSLS) as part of the Dual Energy Digital Subtraction Transvenous Coronary Angiography research program. This program takes place in the Synchrotron Medical Research Facility (SMERF) on the X17B2 wiggler beamline. Encouraged by the success of the initial patient images, the NSLS has recently embarked on an ambitious upgrade effort. This effort covers all aspects of the X17B2 beamline and includes improved radiation shielding, a Laue monochromator assembly, a computer-controlled five motion patient scanning chair assembly, a fast low-noise image acquisition system, and a modularized patient safety system. These improvements will allow major advances in imaging patients based on ECG signal gating and multiple view imaging. Two advanced technology initiatives are underway with industrial collaborators. One will develop real-time image acquisition and display of the subtracted digital images. The second will develop a compact x-ray source of medical imaging. The source will be a linear electron accelerator creating characteristic radiation line emissions.

  18. Multilayer Laue Lens Growth at NSLS-II

    SciTech Connect

    Conley R.; Bouet, N.; Lauer, K.; Carlucci-Dayton, M.; Biancarosa, J.; Boas, L.; Drannbauer, J.; Feraca, J.; Rosenbaum, L.

    2012-08-15

    The new NSLS-II deposition laboratory has been commissioned to include a variety of thin-film characterization equipment and a next-generation deposition system. The primary goal for this effort is R&D on the multilayer Laue lens (MLL), which is a new type of x-ray optic with the potential for an unprecedented level of x-ray nano-focusing. This unique deposition system contains many design features in order to facilitate growth of combined depth-graded and laterally graded multilayers with precise thickness control over many thousands of layers, providing total film growth in one run of up to 100 {micro}m thick or greater. A precision in-vacuum linear motor servo system raster scans a substrate over an array of magnetrons with shaped apertures at well-defined velocities to affect a multilayer coating. The design, commissioning, and performance metrics of the NSLS-II deposition system will be discussed. Latest growth results of both MLL and reflective multilayers in this machine will be presented.

  19. Commissioning and Early Operation for the NSLS-II Booster RF System

    SciTech Connect

    Marques, C.; Cupolo, J.; Davila, P.; Gao, F.; Goel, A.; Holub, B.; Kulpin, J.; McDonald, K.; Oliva, J.; Papu, J.; Ramirez, G.; Rose, J.; Sikora, R.; Sorrentino, C.; Towne, N.

    2015-05-03

    The National Synchrotron Light Source II (NSLS-II) at Brookhaven National Laboratory (BNL) is a third generation 3GeV, 500mA synchrotron light source. We discuss the booster synchrotron RF system responsible for providing power to accelerate an electron beam from 200MeV to 3GeV. The RF system design and construction are complete and is currently in the operational phase of the NSLS-II project. Preliminary operational data is also discussed.

  20. The NSLS-II Multilayer Laue Lens Deposition System

    SciTech Connect

    Conley, R.; Bouet, N.; Biancarosa, J.; Shen, Q.; Boas, L.; Feraca, J.; Rosenbaum, L.

    2009-08-02

    The NSLS-II[1] program has a requirement for an unprecedented level of x-ray nanofocusing and has selected the wedged multilayer Laue lens[2,3] (MLL) as the optic of choice to meet this goal. In order to fabricate the MLL a deposition system is required that is capable of depositing depth-graded and laterally-graded multilayers with precise thickness control over many thousands of layers, with total film growth in one run up to 100m thick or greater. This machine design expounds on the positive features of a rotary deposition system[4] constructed previously for MLLs and will contain multiple stationary, horizontally-oriented magnetron sources where a transport will move a substrate back and forth in a linear fashion over shaped apertures at well-defined velocities to affect a multilayer coating.

  1. Closed-orbit correction of the NSLS VUV ring

    SciTech Connect

    Bozoki, E.; Bittner, J.; Blumberg, L.; Dickinson, T.; Galayda, J.

    1983-01-01

    We describe the results obtained from the orbit correction system in the NSLS VUV storage ring which consists of 24 PUE stations and 16 horizontal and vertical correction dipoles. The data were obtained by the PUEREAL module of the RING control program which provides automatic switching of the signal from individual electrodes of the PUE stations and provides a readout at harmonic of the rf frequency. The closed orbit is then calculated and corrected by measured displacements of the PUE's from the adjacent quadrupoles. The ORBIT module of the RING program was used to minimize the RMS orbit deviations choosing the most effective correctors and calculating their strengths. For the horizontal case, the correction was accomplished using 3 correctors in two iterations starting with RMS values X = 2.9 mm to X = 0.9 mm. Vertically three iterations and 6 correctors were required to correct the RMS value from Z = 6.8 nm to Z = 0.8 mm.

  2. INSERTION DEVICES R AND Ds FOR NSLS-II.

    SciTech Connect

    TANABE,T.; HARDER, D.A.; RAKOWSKY, G.; SHAFTAN, T.; SKARITKA, J.

    2007-06-25

    NSLS-II is a medium energy storage ring of 3GeV electron beam energy with sub-nm.rad horizontal emittance and top-off capability at 500mA. Damping wigglers will be used not only to reduce the beam emittance but also for broadband sources for users. Cryo-Permanent Magnet Undulators (CPMUs) are considered for hard X-ray linear device, and permanent magnet based Elliptically Polarized Undulators (EPUs) are for polarization control. Rigorous R&D plans have been established to pursue the performance enhancement of the above devices as well as building new types of insertion devices such as high temperature superconducting wiggler/undulators. This paper describes the details of these activities and discuss technical issues.

  3. The NSLS VUV undulator: Spectral characteristics and operating experience

    SciTech Connect

    Johnson, P.D.; Galayda, J.; Hulbert, S.L.; Klaffky, R.W.; Luccio, A.; Vignola, G.; Jacobsen, C.

    1987-01-01

    The design and operating characteristics of the VUV undulator installed on the NSLS VUV ring are presented. Specifically, the spectral output through three circular on-axis pinholes of different diameters has been measured. Near the minimum magnetic gap (40mm), the flux into a 0.25 mrad circular aperture at the peak of the fundamental (h..nu.. = 57 eV) is approx.1 /times/ 10/sup 14/ photonssec0.1A1%BW. We find good agreement in spectral shape between these measured spectra and spectra calculated by integrating the theoretical undulator emission spectrum over the relevant spatial variables and including electron beam emittance. We also show calculated zero-emittance and on-axis flux spectra for comparison. A description is given of the beam line and monochromator currently installed on this undulator for the purpose of performing spin-resolved photoemission.

  4. NSLS IN-VACUUM UNDULATORS AND MINI-BETA STRAIGHTS.

    SciTech Connect

    RAKOWSKY,G.; LYNCH,D.; BLUM,E.B.; KRINSKY,S.

    2001-06-18

    We review the work carried out in the X13 R&D Straight Section of the NSLS X-Ray Ring on small gap in-vacuum undulators (IVUNs). Then we discuss: (1) plans to replace the pure permanent magnet undulator in X13 by a hybrid design providing stronger magnetic fields, enhancing the tunability of the device; (2) plans to install hybrid IVUNs in the two RF straights of the X-Ray Ring, increasing the number of insertion devices in the XRay Ring to eight; (3) the possibility of reducing the vertical beta function in the X13 straight from 0.33 m down to 0.16 m. This reduction in beta function would allow us to decrease the usable undulator gap from 3mm down to 2mm, further increasing the tuning range.

  5. Polarized wiggler for NSLS x-ray ring design considerations

    SciTech Connect

    Friedman, A.; Krinsky, S.; Blum, E.

    1992-03-01

    We examine the properties of an elliptically polarized wiggler that will generate circularly polarized photons with energy spectrum of 3--12 KeV. The vertical wiggler magnetic field is produced by permanent magnets while the horizontal wiggler field is generated by electric coils capable of AC excitation. The radiation parameters of the wiggler are presented, including photon flux, circular and linear polarization and spectrum. These parameters are compared to the synchrotron radiation from a bending magnet. Numerical values are calculated for radiation from the wiggler and bending magnet for the NSLS X-ray ring parameters. A conceptual design for such a wiggler is discussed and several different alternatives are analyzed. We consider AC excitation of the wiggler to produce the time modulation of the elliptic polarization, and also to produce time modulated linearly polarized radiation.

  6. High Brightness Electron Beam Studies at the NSLS SDL

    SciTech Connect

    Qian,H.; Hidaka, Y.; Murphy, J. B.; Podobedov, B.; Seletskiy, S.; Shen, Y.; Yang, X.; Wang, X. J.; Tang, C. X.

    2009-05-04

    Experimental optimization of electron beam brightness at the NSLS SDL is reported in this paper. Using a high quantum efficiency (QE) Mg metal cathode and the S-band BNL-type RF gun, we have systematically studied electron beams transverse and longitudinal emittance. The measured thermal emittance for the Mg cathode is 0.85{+-}0.04 mm-mrad/mm, which contradicts the current thermal emittance model. For a 50 pC beam, measured normalized transverse and longitudinal RMS emittance are 0.6 mm-mrd and 5.2 ps-keV, respectively. The smallest projected transverse emittance observed for a 20 pC charge is 0.15 {+-} 0.02 mm-mrad.

  7. ADVANCES IN X-RAY COMPUTED MICROTOMOGRAPHY AT THE NSLS.

    SciTech Connect

    DOWD,B.A.

    1998-08-07

    The X-Ray Computed Microtomography workstation at beamline X27A at the NSLS has been utilized by scientists from a broad range of disciplines from industrial materials processing to environmental science. The most recent applications are presented here as well as a description of the facility that has evolved to accommodate a wide variety of materials and sample sizes. One of the most exciting new developments reported here resulted from a pursuit of faster reconstruction techniques. A Fast Filtered Back Transform (FFBT) reconstruction program has been developed and implemented, that is based on a refinement of the ''gridding'' algorithm first developed for use with radio astronomical data. This program has reduced the reconstruction time to 8.5 sec for a 929 x 929 pixel{sup 2} slice on an R10,000 CPU, more than 8x reduction compared with the Filtered Back-Projection method.

  8. Advances in x-ray computed microtomography at the NSLS

    SciTech Connect

    Dowd, B.A.; Andrews, A.B.; Marr, R.B.; Siddons, D.P.; Jones, K.W.; Peskin, A.M.

    1998-08-01

    The X-Ray Computed Microtomography workstation at beamline X27A at the NSLS has been utilized by scientists from a broad range of disciplines from industrial materials processing to environmental science. The most recent applications are presented here as well as a description of the facility that has evolved to accommodate a wide variety of materials and sample sizes. One of the most exciting new developments reported here resulted from a pursuit of faster reconstruction techniques. A Fast Filtered Back Transform (FFBT) reconstruction program has been developed and implemented, that is based on a refinement of the gridding algorithm first developed for use with radio astronomical data. This program has reduced the reconstruction time to 8.5 sec for a 929 x 929 pixel{sup 2} slice on an R10,000 CPU, more than 8x reduction compared with the Filtered Back-Projection method.

  9. Microspectroscopy of the photosynthetic compartment of algae.

    PubMed

    Evangelista, Valtere; Frassanito, Anna Maria; Passarelli, Vincenzo; Barsanti, Laura; Gualtieri, Paolo

    2006-01-01

    We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of algae belonging to different taxonomic divisions and higher plants. The feasibility of microspectroscopy for discriminating among species and/or phylogenetic groups was tested on laboratory cultures. Gaussian bands decompositions and a fitting algorithm, together with fourth-derivative transformation of absorbance spectra, provided a reliable discrimination among chlorophylls a, b and c, phycobiliproteins and carotenoids. Comparative analysis of absorption spectra highlighted the evolutionary grouping of the algae into three main lineages in accordance with the most recent endosymbiotic theories.

  10. NSLS 2005 ACTIVITY REPORT (NATIONAL SYNCHROTRON LIGHT SOURCE ACTIVITY REPORT 2005).

    SciTech Connect

    MILLER, L.

    2006-05-01

    In 2005, the NSLS proved itself, once again, to be a center of scientific excellence. This remarkable facility, commissioned in the early 1980s, is still attracting some of the world's best researchers in almost every scientific field, who produce more than seven hundred scientific papers every year using the NSLS. The 'Science Highlights' and 'Feature Highlights' sections of this report are just a small sampling of the many, many impressive research projects conducted at the NSLS in 2005. For example, a user group synthesized and studied zinc-oxide nanowires, which have applications in many optical and electrical devices. Another user group studied how strontium and uranium are removed from high-level radioactive waste. And in another interesting study, users deciphered the basis for antibiotic resistance. However, as always, the success of these projects depends on the performance of the facility. Again this year, the rings were in top form--reliability was 96 percent for the x-ray ring and 99 percent for the VUV-IR ring. Additionally, to keep the NSLS as productive as possible and to continue to attract users, many beamline upgrade projects were completed this year. One of the highlights of these upgrades is the new mini-gap undulator installed at beamline X25. This insertion device is providing a much brighter x-ray source for the program at X25. In the always important area of safety, several noteworthy activities took place this year. In particular, NSLS staff made a major commitment to labeling and inspecting electrical equipment. And perhaps the best news is what didn't happen--there were no reportable occurrences related to environmental, safety, or health issues in 2005, and no injuries that resulted in restricted or lost time. We all owe thanks to the dedicated NSLS staff and users who have ensured that the NSLS remains a reliable, safe, up-to-date research facility. As 2005 came to an end, I stepped down as NSLS Chairman in order to focus my primary

  11. Identification of water pathogens by Raman microspectroscopy.

    PubMed

    Kusić, Dragana; Kampe, Bernd; Rösch, Petra; Popp, Jürgen

    2014-01-01

    Legionella species can be found living in water mostly in a viable but nonculturable state or associated with protozoa and complex biofilm formations. Isolation and afterwards identification of these pathogens from environmental samples by using common identification procedures based on cultivation are extremely difficult and prolonged. The development of fast and sensitive method based on the cultivation free identification of bacteria is necessary. In this study Raman microspectroscopy combined with multiclass support vector machines have been used to discriminate between Legionella and other common aquatic bacteria, to distinguish among clinically relevant Legionella species and to classify unknown Raman spectra for a fast and reliable identification. Recorded Raman spectra of the twenty-two Legionella species as well as the Raman spectra of Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa were utilized to build the classification model. Afterwards, independent Raman spectra of eleven species were used to identify them on the basis of the classification model that was created. The present study shows that Raman microspectroscopy can be used as a rapid and reliable method to distinguish between Legionella species recognized as human pathogens and to identify samples which are unknown to the model based on multiclass support vector machines (MC-SVM).

  12. A study of Ganoderma lucidum spores by FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Chen, Xianliang; Qi, Zeming; Liu, Xingcun; Li, Weizu; Wang, Shengyi

    2012-06-01

    In order to obtain unique information of Ganoderma lucidum spores, FTIR microspectroscopy was used to study G. lucidum spores from Anhui Province (A), Liaoning Province (B) and Shangdong Province (C) of China. IR micro-spectra were acquired with high-resolution and well-reproducibility. The IR spectra of G. lucidum spores from different areas were similar and mainly made up of the absorption bands of polysaccharide, sterols, proteins, fatty acids, etc. The results of curve fitting indicated the protein secondary structures were dissimilar among the above G. lucidum spores. To identify G. lucidum spores from different areas, the H1078/H1640 value might be a potentially useful factor, furthermore FTIR microspectroscopy could realize this identification efficiently with the help of hierarchical cluster analysis. The result indicates FTIR microspectroscopy is an efficient tool for identification of G. lucidum spores from different areas. The result also suggests FTIR microspectroscopy is a potentially useful tool for the study of TCM.

  13. Reveal Protein Molecular Structural-Chemical Differrences Between Two Types of Winterfat (Forage) Seeds with Physiological Differences in Low Temperature Tolerance Using Synchrotron-Based Fourier Transform Infrared Microspectroscopy

    SciTech Connect

    Yu,P.; Wang, R.; Bai, Y.

    2005-01-01

    Winterfat (Krascheninnikovia lanata) (forage seed) is a long-lived native shrub with superior forage quality for livestock and wildlife. The objectives of this study were to use advanced synchrotron technology [S-Fourier transform infrared microspectroscopy (FTIR)] as a novel approach to reveal protein molecular structural-chemical differences in terms of protein secondary structures between the two types of winterfat (forage) seeds, which show physiological differences in low-temperature tolerances. This experiment was performed at beamline U10B at the National Synchrotron Light Source NSLS in Brookhaven National Laboratory BNL, U.S. Department of Energy (NSLS-BNL, New York). The results showed that with the synchrotron analytical technique (S-FTIR), the molecular structural-chemical makeup and characteristics of the winterfat seed tissues could be imaged and revealed. The protein secondary structures differed between the large and the small seed tissues. By using the multicomponent peaks modeling method, the results show that the large seeds contained no significant differences (P > 0.05) in percentage of {beta}-sheet (average 37.0%) and {alpha}-helix (average 24.1%). However, the large seeds contained a lower (P < 0.05) percentage of {beta}-turns (18.1 vs. 20.1%) and a lower (P < 0.05) ratio of {beta}-turns to {alpha}-helices (0.8 vs. 0.9) and {beta}-turns to {beta}-sheets (0.5 vs. 0.6). Our results demonstrate the potential of highly spatially resolved synchrotron-based FTIR microspectroscopy to reveal differences of structural molecular chemistry and protein secondary structures, which are associated with seed size variation and may affect germination behaviors.

  14. Multi-Photon Micro-Spectroscopy of Biological Specimens

    DTIC Science & Technology

    2000-07-01

    Arabidopsis thaliana and maize stem sections were used to demonstrate the feasibility of multi- photon fluorescence micro-spectroscopy at subcellular...Micro-spectroscopy, multi-photon fluorescence spectroscopy, second harmonic generation, plant tissues, stem, chloroplast, protoplast, maize , Arabidopsis...thaliana and stem slices of maize (Zea mays) were used as samples to address these issues in a set-up for micro-spectroscopy. 2. MATERIALS AND METHODS

  15. Molecular imaging with CARS micro-spectroscopy.

    PubMed

    Cicerone, Marcus

    2016-08-01

    After more than a decade of instrument and method development, broadband coherent anti-Stokes Raman scattering (CARS) micro-spectroscopy is beginning to live up to its potential as a label-free imaging modality that can rapidly generate high resolution images with full vibrational spectra at each image pixel. Presently these instruments are able to obtain quantitative, spatially resolved information on lipids from the CH stretch region of the Raman spectrum, and some instrument designs facilitate acquisition of high quality fingerprint spectra, containing information on a host of molecular species including structural proteins, nucleotides, and metabolites. While most of the existing instruments are research projects themselves, it appears that the relevant technologies are maturing so that commercially available instruments may not be too far in the future, making this remarkable imaging modality widely available. Published by Elsevier Ltd.

  16. Analysis of human hair by Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Plascencia-Castro, A. S.; Cordova-Fraga, T.; Piña-Ruiz, A. L.; Hernández-Rayas, A.; Bernal, J. J.

    2017-04-01

    Raman microspectroscopy is an optical compound identification technique, which is widely used nowadays for different field applications. A crucial part of this technique is the focus given to the sample in the microscope because it depends on which part of the sample it will analyze. In this work, the effects of irradiating a natural hair samples, obtained from women aged 18 to 55, with a monochromatic light of the Raman spectrometer in two different focus is presented. Two different spectra were obtained with a peak in common. Depending on the information wanted, how the sample is focused plays a crucial role, either way the spectra is information-rich and may be used for biomedical applications.

  17. Analysis of Allergenic Pollen by FTIR Microspectroscopy.

    PubMed

    Zimmerman, B; Tafintseva, V; Bağcıoğlu, M; Høegh Berdahl, M; Kohler, A

    2016-01-05

    Fourier transform infrared (FTIR) spectroscopy is a powerful tool for the identification and characterization of pollen and spores. However, interpretation and multivariate analysis of infrared microscopy spectra of single pollen grains are hampered by Mie-type scattering. In this paper, we introduce a novel sampling setup for infrared microspectroscopy of pollens preventing strong Mie-type scattering. Pollen samples were embedded in a soft paraffin layer between two sheets of polyethylene foils without any further sample pretreatment. Single-grain infrared spectra of 13 different pollen samples, belonging to 11 species, were obtained and analyzed by the new approach and classified by sparse partial least-squares regression (PLSR). For the classification, chemical and physical information were separated by extended multiplicative signal correction and used together to build a classification model. A training set of 260 spectra and an independent test set of 130 spectra were used. Robust sparse classification models allowing the biochemical interpretation of the classification were obtained by the sparse PLSR, because only a subset of variables was retained for the analysis. With accuracy values of 95% and 98%, for the independent test set and full cross-validation respectively, the method is outperforming the previously published studies on development of an automated pollen analysis. Since the method is compatible with standard air-samplers, it can be employed with minimal modification in regular aerobiology studies. When compared with optical microscopy, which is the benchmark method in pollen analysis, the infrared microspectroscopy method offers better taxonomic resolution, as well as faster, more economical, and bias-free measurement.

  18. Beam Loss Monitors for NSLS-II Storage Ring

    SciTech Connect

    Kramer, S.L.; Cameron, P.

    2011-03-28

    The shielding for the NSLS-II storage ring will provide adequate protection for the full injected beam losses in two cells of the ring around the injection point, but the remainder of the ring is shielded for lower losses of <10% top-off injection beam current. This will require a system to insure that beam losses do not exceed levels for a period of time that could cause excessive radiation exposure outside the shield walls. This beam Loss Control and Monitoring system will have beam loss monitors that will measure where the beam charge is lost around the ring, to warn operators if losses approach the design limits. To measure the charge loss quantitatively, we propose measuring the electron component of the shower as beam electrons hit the vacuum chamber (VC) wall. This will be done using the Cerenkov light as electrons transit ultra-pure fused silica rods placed close to the inner edge of the VC. The entire length of the rod will collect light from the electrons of the spread out shower resulting from the small glancing angle of the lost beam particles to the VC wall. The design and measurements results of the prototype Cerenkov BLM will be presented.

  19. Flexibility in the Design of the NSLS-II Lattice

    SciTech Connect

    Kramer,S.L.; Guo, W.

    2009-05-04

    The NSLS-II light source is a proposed 3 GeV storage ring, with the potential for ultra-low emittance [1]. The lattice design uses a 30 cell DBA structure with a periodicity of 15, with alternating long and short straight sections. All cells are tuned achromatic to maximize the emittance reduction achieved as damping wigglers are added to the ring. Recent optimization of the lattice consisted of increasing the number of possible hard X-ray beam ports using three pole wigglers, reducing the number of magnets (quadrupoles and sextupoles) and shifting the magnets to allow easier extraction of the photon beams. The impact of the reduction of magnets on the lattice flexibility will be presented in terms of the tuning range possible for the lattice parameters: tune, emittance, chromaticity, and beta function matching to user insertion devices (IDs). This flexibility is important for optimizing the lattice linear and nonlinear properties, the dynamic aperture, and its impact on beam lifetime, as well as matching the user source requirements and for value engineering of magnets and power supplies.

  20. Parametric Optimization of Undulators for NSLS-II Project Beamlines

    NASA Astrophysics Data System (ADS)

    Chubar, O.; Bengtsson, J.; Berman, L.; Broadbent, A.; Cai, Y. Q.; Hulbert, S.; Shen, Q.; Tanabe, T.

    2010-06-01

    General optimization procedure, computation methods used, and the obtained optimal parameters of undulators for the NSLS-II project beamlines are reported. The optimization starts with high-accuracy calculation of undulator magnetic fields, using Radia magnetostatics code, for a large set of periods and vertical gaps of a given undulator type, given magnetic materials and a scalable magnet geometry. From the resulting magnetic fields, a sub-set of undulator periods and the corresponding vertical gaps, providing the required low-energy cut-off values of spectral harmonics for each particular beamline, is determined. In parallel, from the same Radia undulator models, angular magnetic kick maps are calculated, and the insertion device effect on electron beam is simulated using Tracy-2 tracking code based on symplectic integrator. After these simulations, magnet parameters are fine-tuned and the maximal acceptable undulator lengths are determined for different straight sections, as functions of minimal gap and with due regard for the electron beam vertical "stay clear" constraint in the case of in-vacuum undulators. Finally, the optimal undulator period and length are determined as the values providing maximal spectral flux among the pre-selected undulator cases, already satisfying the requirements concerning the harmonic cut-off values and the effect on electron beam.

  1. NSLS-II X-Ray Diagnostics Development

    SciTech Connect

    ILINSKI, P.

    2011-03-28

    NSLS-II x-ray diagnostics will provide continuous online data of electron beam dimensions, which will be used to derive electron beam emittance and energy spread. It will also provide information of electron beam tilt for coupling evaluation. X-ray diagnostics will be based on imaging of bending magnet and three-pole wiggler synchrotron radiation sources. Diagnostics from three-pole wiggler source will be used to derive particles energy spread. Beta and dispersion functions will have to be evaluated for emittance and particles energy spread calculations. Due to small vertical source sizes imaging need to be performed in x-ray energy range. X-ray optics with high numerical aperture, such as compound refractive lens, will be used to achieve required spatial resolution. Optical setups with different magnifications in horizontal and vertical directions fill be employed to deal with large aspect ratio of the source. X-ray diagnostics setup will include x-ray imaging optics, monochromatization, x-ray imaging and recording components.

  2. Beam Loss Control for the NSLS-II Storage Ring

    SciTech Connect

    Kramer, S.L.; Choi, J.

    2011-03-28

    The shielding design for the NSLS-II storage ring is designed for the full injected beam losses in two periods of the ring around the injection point, but for the remainder of the ring its shielded for {le} 10% top-off injection beam. This will require a system to insure that beam losses do not exceed these levels for time sufficient to cause excessive radiation exposure outside the shield walls. This beam Loss Control and Monitoring (LCM) system will control the beam losses to the more heavily shielded injection region while monitoring the losses outside this region. To achieve this scrapers are installed in the injection region to intercept beam particles that might be lost outside this region. The scrapers will be thin (< 1Xrad) that will allow low energy electrons to penetrate and the subsequent dipole will separate them from the stored beam. These thin scrapers will reduce the radiation from the scraper compared to thicker scrapers. The dipole will provide significant local shielding for particles that hit inside the gap and a source for the loss monitor system that will measure the amount of beam lost in the injection region.

  3. Achieving Vibration Stability of the NSLS-II Hard X-ray Nanoprobe Beamline

    SciTech Connect

    Simos, N.; Chu, Y. S.; Broadbent, A.; Nazaretski, E.; Margulies, L.; Dyling, O.; Shen, Q.; Fallier, M.

    2011-09-09

    The hard x-ray nanoprobe (HXN) beamline of the National Synchrotron Light Source II (NSLS-II) requires high levels of stability in order to achieve the desired instrument resolution. To ensure that the design of the endstation helps meet the stringent criteria and that natural and cultural vibration is mitigated both passively and actively, a comprehensive study complimentary to the design process has been undertaken. Vibration sources that have the potential to disrupt sensitive experiments such as wind, traffic, and NSLS II operating systems have been studied using state-of-the-art simulations and an array of field data. Further, final stage vibration isolation principles have been explored.

  4. Achieving Vibration Stability of the NSLS-II Hard X-ray Nanoprobe Beamline

    NASA Astrophysics Data System (ADS)

    Simos, N.; Chu, Y. S.; Broadbent, A.; Nazaretski, E.; Margulies, L.; Dyling, O.; Shen, Q.; Fallier, M.

    2011-09-01

    The hard x-ray nanoprobe (HXN) beamline of the National Synchrotron Light Source II (NSLS-II) requires high levels of stability in order to achieve the desired instrument resolution. To ensure that the design of the endstation helps meet the stringent criteria and that natural and cultural vibration is mitigated both passively and actively, a comprehensive study complimentary to the design process has been undertaken. Vibration sources that have the potential to disrupt sensitive experiments such as wind, traffic, and NSLS II operating systems have been studied using state-of-the-art simulations and an array of field data. Further, final stage vibration isolation principles have been explored.

  5. NSLS 2006 ACTIVITY REPORT (NATIONAL SYNCHROTRON LIGHT SOURCE ACTIVITY REPORT 2006)

    SciTech Connect

    MILLER, L.

    2006-12-31

    This past year has seen both challenges and fantastic new opportunities for the user community at the NSLS. The fantastic new opportunities are clear and abundant. We now have a five-year strategic plan for new development and continued operation of the NSLS. The NSLS continues to be an extremely productive facility, and the UEC is delighted at how NSLS Chair Chi-Chang Kao has consulted widely within the user community to develop a five-year plan for strategic upgrades and continued operation of the facility. The NSLS-II project, led by Associate Lab Director Steve Dierker, has done very well in its Department of Energy (DOE) reviews and will hopefully soon receive Critical Decision-1 (CD-1) approval, which in DOE lingo gives a go-ahead to launch the detailed design of the facility. We also held the first joint user meeting between the NSLS and Brookhaven's Center for Functional Nanomaterials (CFN), for which the building is near completion. The joint user meeting is an important step toward the close collaboration of the two facilities. The CFN, led by Emilio Mendez, promises to provide capabilities and research foci that are complementary to those at the NSLS. Together, all of these developments give a clear path to an exciting future of synchrotron radiation research at Brookhaven! However, with opportunities come challenges! One of the largest of these faced in the past year involved congressional support for scientific research in general, and DOE user facilities in particular. As you likely know, Congress did not complete its usual budget process in 2006, with the exceptions of the departments of Defense and Homeland Security. This left science funding at the budget levels enacted in late 2005 for FY2006, and unfortunately, FY2006 was not a particularly memorable vintage for science support. The good news is that you, the user community, have spoken up with unprecedented vigor about this, and Congress appears to be listening. As we look at the FY2007 budget

  6. NSLS 2007 Activity Report (National Synchrotron Light Source Activity Report 2007)

    SciTech Connect

    Miller ,L.; Nasta, K.

    2008-05-01

    The National Synchrotron Light Source is one of the world's most productive and cost-effective user facilities. With 2,219 individual users, about 100 more than last year, and a record-high 985 publications, 2007 was no exception. In addition to producing an impressive array of science highlights, which are included in this Activity Report, many NSLS users were honored this year for their scientific accomplishments. Throughout the year, there were major strides in the development of the scientific programs by strengthening strategic partnerships with major research resources and with the Center for Functional Nanomaterials (CFN). Of particular note, the Consortium for Materials Properties Research in Earth Sciences (COMPRES) received renewed funding for the next five years through the National Science Foundation. COMPRES operates four high-pressure NSLS beamlines--X17B2, X17B3, X17C, and U2A--and serves the earth science community as well as the rapidly expanding segment of researchers using high-pressure techniques in materials, chemical, and energy-related sciences. A joint appointment was made between the NSLS and Stony Brook University to further enhance interactions with COMPRES. There was major progress on two key beamline projects outlined in the Five-Year Strategic Plan: the X25 beamline upgrade and the construction of the X9 small angle scattering (SAXS) beamline. The X25 overhaul, which began with the installation of the in-vacuum mini-gap undulator (MGU) in January 2006, is now complete. X25 is once again the brightest beamline for macromolecular crystallography at the NSLS, and in tandem with the X29 undulator beamline, it will keep the NSLS at the cutting edge in this important area of research. Upgrade work associated with the new MGU and the front end for the X9 SAXS beamline--jointly developed by the NSLS and the CFN--also was completed. Beamline X9 will host the SAXS program that currently exists at beamline X21 and will provide new microbeam SAXS

  7. Design of coupler for the NSLS-II storage ring superconducting RF cavity

    SciTech Connect

    Yeddulla, M.; Rose, J.

    2011-03-28

    NSLS-II is a 3GeV, 500mA, high brightness, 1 MW beam power synchrotron facility that is designed with four superconducting cavities working at 499.68 MHz. To operate the cavities in over-damped coupling condition, an External Quality Factor (Qext) of {approx}65000 is required. We have modified the existing coupler for the CESR-B cavity which has a Qext of {approx}200,000 to meet the requirements of NSLS-II. CESR-B cavity has an aperture coupler with a coupler 'tongue' connecting the cavity to the waveguide. We have optimized the length, width and thickness of the 'tongue' as well as the width of the aperture to increase the coupling using the three dimensional electromagnetic field solver, HFSS. Several possible designs will be presented. We have modified the coupler of the CESR-B cavity to be used in the storage ring at the NSLS-II project using HFSS and verified using CST Microwave Studio. Using a combination of increasing the length and width of the coupler tongue and increasing the width of the aperture, the external Q of the cavity coupler was decreased to {approx}65000 as required for the design of the NSLS-II storage ring design.

  8. Evaluation of Pinhole Camera Resolution for NSLS-II Storage Ring

    SciTech Connect

    Pinayev,I.

    2008-05-04

    The NSLS-II Storage Ring provides ultrabright radiation sources with extra-small sizes of the circulating electron beam. The beam dimensions will be monitored with a pinhole camera. In this paper they discuss the possible design and ultimate achievable resolution of the system. Modeling is based on the SRW code as well as numerical calculations using MATLAB.

  9. Software environment and configuration for the DSP controlled NSLS booster power supplies

    SciTech Connect

    Olsen, R.; Dabrowski, J.; Murray, J.

    1993-07-01

    The booster at the NSLS is being upgraded from 0.75 to 2 pulses per second by means of the installation of new dipole, quadrupole, and sextupole power supplies. The control system of these power supplies employs general purpose digital signal processing modules, and therefore, software support is required. This paper outlines the development system configuration, and the software environment.

  10. Confocal Raman microspectroscopy of the skin.

    PubMed

    Förster, Matthias; Bolzinger, Marie-Alexandrine; Montagnac, Gilles; Briançon, Stéphanie

    2011-01-01

    Confocal Raman spectroscopy is a technique with considerable potential for the non-invasive study of biological tissues and skin samples in vitro or in vivo. It can be used to study skin physiology and possible pathological conditions and to obtain data about molecular composition and the structure of skin, for example, water content, moisturization and changes in the skin barrier function can all be observed. In-depth measurements also allow biopharmaceutical studies, such as analyzing the rate of penetration of a drug and the biochemical changes that may be induced by an applied formulation. Confocal Raman microspectroscopy is now at such a stage of refinement that it opens up new vistas. The big leap forward in its ease of use enables this technology to be used as an analytical method by more and more non-specialist laboratories. This review gives an overview of the state of the art of this technology by presenting an update on the principles of Raman spectroscopy and then by looking at examples of new developments in in vivo and in vitro applications.

  11. Ultrasonic microspectroscopy characterization of chemically tempered glass

    NASA Astrophysics Data System (ADS)

    Arakawa, Mototaka; Kushibiki, Jun-ichi; Ohashi, Yuji

    2017-01-01

    We evaluated the elastic properties of the compressive stress (CS) layer of chemically tempered glass by ultrasonic microspectroscopy (UMS) in a very high frequency (VHF) range. Two commercial aluminosilicate glass specimens were prepared, and one of them was chemically tempered. Changes in elastic properties in the CS layer with the residual stress introduced by the exchange of Na+ ions for larger K+ ions were estimated by precisely measuring the densities and longitudinal and shear velocities for both the tempered and nontempered specimens. Using a single-layer model for the surface layer, we observed drastic increases in bulk-wave velocities and significant decreases in attenuation coefficients. We determined that the average elastic properties, namely, the elastic constants c 11 and c 44, and the density of the surface layer, were 9.6 and 7.1, and 1.2% larger than those of the nontempered specimen, respectively. We also estimated the distributions of the elastic properties according to the complementary error function (CEF) for the distribution of K+ ion concentration. Furthermore, using a line-focus-beam (LFB) system, we measured the frequency characteristics of the velocity (V LSAW) of leaky surface acoustic waves (LSAWs) on a water-loaded surface of the tempered specimen and clarified that the distributions of the elastic properties did not follow the CEF. The LFB system can be used for analyzing/determining details of the surface properties and is a promising tool for evaluating and characterizing chemically tempered glass and tempering process conditions.

  12. The Infrared Microspectroscopy Beamline at CAMD

    NASA Astrophysics Data System (ADS)

    Kizilkaya, O.; Singh, V.; Desta, Y.; Pease, M.; Roy, A.; Scott, J.; Goettert, J.; Morikawa, E.; Hormes, J.; Prange, A.

    2007-01-01

    The first infrared microspectroscopy beamline at the Louisiana State University, Center for Advanced Microstructures and Devices (LSU-CAMD) has been constructed and dedicated to investigation of samples from various disciplines including chemistry, geology, biology, and material sciences. The beamline comprises a simple optical configuration. A planar and toroidal mirror pair collects 50 and 15 mrad synchrotron radiation in horizontal and vertical directions, respectively, and focuses the beam through a diamond window located outside of the shielding wall. This focus acts as a new source point for the rest of the optical systems. The synchrotron beam spot size of 35 μm and 12 μm is measured in the x and y direction of the sample stage position of the microscope. This small beam spot has a superior brightness compared to conventional IR sources and allows spatially resolved measurements with very good signal/noise ratio. Compared to a conventional thermal source, synchrotron radiation provides 30 times better intensity and a two orders of magnitude greater signal/noise ratio when measuring with microscope aperture size of 15 × 15 μm2. The results of the studies on the fungus-plant interaction with its resultant effects on the healthy leaves, and bacterial growth process in the crystallization of gordaite, a mineral, are presented.

  13. Raman microspectroscopy for visualization of peripheral nerves

    NASA Astrophysics Data System (ADS)

    Minamikawa, Takeo; Harada, Yoshinori; Koizumi, Noriaki; Takamatsu, Tetsuro

    2013-02-01

    The peripheral nervous system plays an important role in motility, sensory, and autonomic functions of the human body. Preservation of peripheral nerves in surgery is essential for improving quality of life of patients. To preserve peripheral nerves, detection of ne peripheral nerves that cannot be identi ed by human eye or under white light imaging is necessary. In this study, we sought to provide a proof-of-principle demonstration of a label-free detection technique of peripheral nerve tissues against adjacent tissues that employs spontaneous Raman microspectroscopy. A line-illumination confocal Raman microscope was used for the experiment. A laser operating at the wavelength of 532 nm was used as an excitation laser light. We obtained Raman spectra of peripheral nerve, brous connective tissue, skeletal muscle, blood vessel, and adipose tissue of Wistar rats, and extracted speci c spectral features of peripheral nerves and adjacent tissues. By applying multivariate image analysis, peripheral nerves were clearly detected against adjacent tissues without any preprocessing neither xation nor staining. These results suggest the potential of the Raman spectroscopic observation for noninvasive and label-free nerve detection, and we expect this method could be a key technique for nerve-sparing surgery.

  14. FT-IR microspectroscopy for microbiological studies.

    PubMed

    Orsini, F; Ami, D; Villa, A M; Sala, G; Bellotti, M G; Doglia, S M

    2000-09-01

    In this article we present an infrared microspectroscopic investigation on Candida albicans microcolonies, taken as a model system for studies on other microorganisms. Excellent Fourier transform infrared (FT-IR) absorption spectra from 4000 to 850 cm(-1) have been collected in only 20 s from sampling areas of 100x100 microm(2) in microcolonies, which had been transferred from the agar plate onto zinc selenide (ZnSe) windows. When different regions within a single microcolony were investigated, absorption spectra with important differences in the carbohydrate absorption (from 1200 to 850 cm(-1)) were detected for the cells in the center and in the periphery of the colony. Results obtained on microcolonies grown on solid agar with increasing dextrose concentrations indicated that the observed spectral heterogeneity was related to differences in dextrose uptake, which was lower for the old cells in the center of the colony than for the metabolically active cells at the periphery. Although it is otherwise difficult to quantitatively evaluate the dextrose uptake in a microcolony, FT-IR absorption microspectroscopy offers a new and rapid method for the analysis of this process. The possibility of studying highly absorbing colonies by attenuated total reflection (ATR) by means of an ATR microscope germanium objective is also presented here for the first time. An evaluation of the contact area sampled by this technique is reported with a discussion of the spatial resolution, the quality and the potential of the ATR measurements.

  15. The Infrared Microspectroscopy Beamline at CAMD

    SciTech Connect

    Kizilkaya, O.; Singh, V.; Desta, Y.; Pease, M.; Roy, A.; Scott, J.; Goettert, J.; Morikawa, E.; Hormes, J.; Prange, A.

    2007-01-19

    The first infrared microspectroscopy beamline at the Louisiana State University, Center for Advanced Microstructures and Devices (LSU-CAMD) has been constructed and dedicated to investigation of samples from various disciplines including chemistry, geology, biology, and material sciences. The beamline comprises a simple optical configuration. A planar and toroidal mirror pair collects 50 and 15 mrad synchrotron radiation in horizontal and vertical directions, respectively, and focuses the beam through a diamond window located outside of the shielding wall. This focus acts as a new source point for the rest of the optical systems. The synchrotron beam spot size of 35 {mu}m and 12 {mu}m is measured in the x and y direction of the sample stage position of the microscope. This small beam spot has a superior brightness compared to conventional IR sources and allows spatially resolved measurements with very good signal/noise ratio. Compared to a conventional thermal source, synchrotron radiation provides 30 times better intensity and a two orders of magnitude greater signal/noise ratio when measuring with microscope aperture size of 15 x 15 {mu}m{sup 2}. The results of the studies on the fungus-plant interaction with its resultant effects on the healthy leaves, and bacterial growth process in the crystallization of gordaite, a mineral, are presented.

  16. Biomedical investigations using Fourier transform-infrared microspectroscopy.

    PubMed

    Bunaciu, Andrei A; Fleschin, Şerban; Aboul-Enein, Hassan Y

    2014-01-01

    One of the most exciting recent developments in infrared spectroscopy has been the coupling of the spectrometer to an infrared microscope. The combination of the new infrared spectrometer and a microscope was a natural thought of scientists in these fields. This development has been so rewarding and so useful in solving today's chemical problems that infrared microspectroscopy has quickly become a significant subclassification of infrared spectroscopy. Infrared microspectroscopy has a much longer history than the recent enthusiasm would imply, however. The great interest in the use of infrared spectroscopy to solve biomedical problems that occurred in recent years shortly spread into the medical and biological fields. The aim of this review is to discuss the new developments in applications of FT-IR microspectroscopy in biomedical analysis, covering the period between 2008 and 2013.

  17. Applications Of Microspectroscopy In The Near-Infrared Region

    NASA Astrophysics Data System (ADS)

    Smith, Matthew J.; Carl, Richard T.

    1989-12-01

    The technique of infrared microspectroscopy has numerous applications in many fields including materials science, forensics, contamination analysis and biological science. The majority of these applications have been in the mid-infrared since using different spectral ranges in an FT-IR spectrometer often involve modifications to the interferometer, source and detector. However, recent advancements in infrared instrumentation have allowed rapid spectral range changes to become routine. As a result, near-infrared microspectroscopy is now a viable technique.1 The principle advantage of near-infrared microspectroscopy is the ability to analyze samples which are totally absorbing in the mid-infrared region. Most near-infrared absorbances are due to overtones or combination bands of fundamental bands and are typically one to two orders of magnitude weaker than their corresponding fundamental transitions. Thus, transmission analysis in the near-infrared can be carried out on many samples which are otherwise too thick for transmission analysis in the mid-infrared.

  18. Development of the XFP beamline for x-ray footprinting at NSLS-II

    SciTech Connect

    Bohon, Jen Sullivan, Michael; Abel, Don; Toomey, John; Chance, Mark R.; Dvorak, Joseph

    2016-07-27

    For over a decade, synchrotron-based footprinting studies at the NSLS X28C beamline have provided unique insights and approaches for examining the solution-state structures of large macromolecular assemblies, membrane proteins, and soluble proteins, for time-resolved studies of macromolecular dynamics, and most recently for in vivo studies of RNA-protein complexes. The transition from NSLS to NSLS-II has provided the opportunity to create an upgraded facility for the study of increasingly complex systems; progress on the development of the XFP (X-ray Footprinting for In Vitro and In Vivo Structural Studies of Biological Macromolecules) beamline at NSLS-II is presented here. The XFP beamline will utilize a focused 3-pole wiggler source to deliver a high flux density x-ray beam, where dynamics can be studied on the microsecond to millisecond timescales appropriate for probing biological macromolecules while minimizing sample perturbation. The beamline optics and diagnostics enable adaptation of the beam size and shape to accommodate a variety of sample morphologies with accurate measurement of the incident beam, and the upgrades in sample handling and environment control will allow study of highly sensitive or unstable samples. The XFP beamline is expected to enhance relevant flux densities more than an order of magnitude from that previously available at X28C, allowing static and time-resolved structural analysis of highly complex samples that have previously pushed the boundaries of x-ray footprinting technology. XFP, located at NSLS-II 17-BM, is anticipated to become available for users in 2016.

  19. Analytical Capabilities of Coherent Anti-Stokes Raman Scattering Microspectroscopy

    PubMed Central

    Arora, Rajan; Petrov, Georgi I.; Yakovlev, Vladislav V.

    2009-01-01

    Nonlinear Raman scattering is an emerging spectroscopy technique for non-invasive microscopic imaging. It can produce a fluorescence background free vibrational spectrum from a microscopic volume of a sample providing chemically specific information about its molecular composition. We analyze the ability of nonlinear Raman microspectroscopy to detect low concentrated molecular species and evaluate its applicability to study complex solutions. PMID:19727338

  20. NSLS-II: Nonlinear Model Calibration for Synchrotrons

    SciTech Connect

    Bengtsson, J.

    2010-10-08

    This tech note is essentially a summary of a lecture we delivered to the Acc. Phys. Journal Club Apr, 2010. However, since the estimated accuracy of these methods has been naive and misleading in the field of particle accelerators, i.e., ignores the impact of noise, we will elaborate on this in some detail. A prerequisite for a calibration of the nonlinear Hamiltonian is that the quadratic part has been understood, i.e., that the linear optics for the real accelerator has been calibrated. For synchrotron light source operations, this problem has been solved by the interactive LOCO technique/tool (Linear Optics from Closed Orbits). Before that, in the context of hadron accelerators, it has been done by signal processing of turn-by-turn BPM data. We have outlined how to make a basic calibration of the nonlinear model for synchrotrons. In particular, we have shown how this was done for LEAR, CERN (antiprotons) in the mid-80s. Specifically, our accuracy for frequency estimation was {approx} 1 x 10{sup -5} for 1024 turns (to calibrate the linear optics) and {approx} 1 x 10{sup -4} for 256 turns for tune footprint and betatron spectrum. For a comparison, the estimated tune footprint for stable beam for NSLS-II is {approx}0.1. Since the transverse damping time is {approx}20 msec, i.e., {approx}4,000 turns. There is no fundamental difference for: antiprotons, protons, and electrons in this case. Because the estimated accuracy for these methods in the field of particle accelerators has been naive, i.e., ignoring the impact of noise, we have also derived explicit formula, from first principles, for a quantitative statement. For e.g. N = 256 and 5% noise we obtain {delta}{nu} {approx} 1 x 10{sup -5}. A comparison with the state-of-the-arts in e.g. telecomm and electrical engineering since the 60s is quite revealing. For example, Kalman filter (1960), crucial for the: Ranger, Mariner, and Apollo (including the Lunar Module) missions during the 60s. Or Claude Shannon et al

  1. Considerations for NSLS-II Synchrotron Radiation Protection When Operating Damping Wigglers at Low Machine Energy

    SciTech Connect

    Seletskiy, S.; Podobedov, B.

    2015-12-30

    The NSLS-II storage ring vacuum chamber, including frontends (FE) and beamlines (BL), is protected from possible damage from synchrotron radiation (SR) emitted from insertion devices (IDs) by a dedicated active interlock system (AIS). The system monitors electron beam position and angle and triggers a beam dump if the beam orbit is outside of the active interlock envelope (AIE). The AIE was calculated under the assumptions of 3 GeV beam energy and ID gaps set to their minimum operating values (i.e. “fully closed”). Recently it was proposed to perform machine studies that would ramp the stored beam energy significantly below the nominal operational value of 3 GeV. These studies may potentially include the use of NSLS-II damping wigglers (DWs) for electron beam emittance reduction and control.

  2. Achieving Vibration Stability of the NSLS-II Hard X-ray Nanoprobe Beamline

    SciTech Connect

    Simos, N.; Chu, Y. N.; Broadbent, A.; Nazaretski, E.; Margulies, L.; Dyling, O.; Shen, Q.; Fallier, M.

    2010-08-30

    The Hard X-ray Nanoprobe (HXN) Beamline of National Synchrotron Light Source II (NSLS-lI) requires high levels of stability in order to achieve the desired instrument resolution. To ensure that the design of the endstation helps meet the stringent criteria and that natural and cultural vibration is mitigated both passively and actively, a comprehensive study complimentary to the design process has been undertaken. Vibration sources that have the potential to disrupt sensitive experiments such as wind, traffic and NSLS II operating systems have been studied using state of the art simulations and an array of field data. Further, final stage vibration isolation principles have been explored in order to be utilized in supporting endstation instruments. This paper presents results of the various study aspects and their influence on the HXN design optimization.

  3. Use of a miniature Toroidal Grating Monochromator on the FEL Undulator at the NSLS

    SciTech Connect

    Johnson, P.D.; Hulbert, S.L.; Howells, M.R.

    1984-01-01

    The use of a miniature Toroidal Grating Monochromator is described which we intend to use to monochromatize the radiation from the free electron laser (FEL) Undulator at the NSLS. Some of the properties of Undulators are described with reference to the design of beamlines and review the properties of TGM's. The results of ray tracing a beamline using such a device and estimates of the expected flux are given.

  4. Magnet power supply control of the NSLS VUV and x-ray storage rings transfer lines

    SciTech Connect

    Klein, J.D.; Ramamoorthy, S.; Singh, O.; Smith, J.D.

    1985-01-01

    The transfer lines for NSLS VUV and x-ray storage rings have been split. New power supplies have been incorporated with existing ones. The existing microprocessor system has been upgraded in order to control the additional functions. This system expands the input/output port of the microprocessor to an addressable serial/parallel link to each magnet power supply. The implementation of this system will be discussed.

  5. Magnetic measurements on an in-vacuum undulator for the NSLS x-ray ring

    SciTech Connect

    Rakowsky, G.; Aspenleiter, J.J.; Graves, W.S.

    1997-07-01

    Magnetic measurements have been performed on the In-Vacuum Undulator (IVUN), built jointly by BNL and SPring-8 for the NSLS X-ray Ring. The IVUN magnet has a Halback-type, pure-permanent magnet structure with a period of 11 mm and a minimum gap of 2 mm. Results of magnetic measurements utilizing Hall probe, moving wire and pulsed wire techniques will be presented and compared.

  6. CURRENT STATUS OF INSERTION DEVICE DEVELOPMENT AT THE NSLS-II AND ITS FUTURE PLANS

    SciTech Connect

    Tanabe, T.; Chubar, O.; Corwin, T.; Harder, D.A.; He, P.; Kitegi, C.; Rank, J.; Rhein, C.; Rakowsky, G.; Spataro, C.

    2011-03-28

    National Synchrotron Light Source-II (NSLS-II) project is currently under construction. Procurement of various insertion devices (IDs) has begun. This ring assumes a very high beam stability requirement which imposes tighter field specifications on insertion devices (IDs) compared to the rings of previous generation. The state of the art ID Magnetic Measurement Facility is being set up in order to be able to certify the stringent requirements on the magnetic field of NSLS-II IDs. The IDs in the project baseline scope include six 3.5m long damping wigglers (DWs) with 100mm period length and 15mm pole gap, two 2.0m Elliptically Polarizing Undulator (EPU) with 49mm period and 11.5mm minimum magnetic gap, two 3.0m long 20mm period and one 1.5m long 21mm period IVU, which the minimum gap of these is 5mm and 5.5mm, respectively. Recently a special device for inelastic X-ray scattering (IXS) beamline has been added to the collection of baseline devices. Three pole wigglers with a 28mm magnetic gap and a peak field over 1 Tesla will be utilized to accommodate the users of the type of radiation which is currently produced with bending magnets at the NSLS.

  7. Experimental evidence of ion-induced instabilities in the NSLS-II storage ring

    NASA Astrophysics Data System (ADS)

    Cheng, Weixing; Li, Yongjun; Podobedov, Boris

    2017-07-01

    Fast ion instability has been identified as one of the most prominent instabilities in the recently constructed NSLS-II storage ring at Brookhaven National Laboratory. At a relatively low beam current ( 25 mA) multi-bunch fills, ion-induced instabilities have already been observed during the early stages of machine commissioning. At present user operation with 250 mA in 1000 bunches, the fast ion still remains the dominant instability, even after months of vacuum conditioning at high current. Ion-induced dipole motions of the electron beam have been suppressed using the transverse bunch-by-bunch (BxB) feedback system. However other adverse effects of this instability, such as the vertical beam size increase along the bunch train cannot be cured by the feedback system. Therefore, to achieve the NSLS-II design current of 500 mA while maintaining a small vertical beam emittance, it is important to further understand the fast ion instability and develop mitigation techniques. This paper reports on a series of ion-instability observations at various fill patterns and beam currents using start-of-art NSLS-II diagnostic tools.

  8. PROGRESS ON INSERTION DEVICE RELATED ACTIVITIES AT THE NSLS-II AND ITS FUTURE PLANS

    SciTech Connect

    Tanabe, T.; Chubar, O.; Corwin, T.; Harder, D. A.; He, P.; Rank, J.; Rakowsky, G.; Spataro, C.

    2010-05-23

    National Synchrotron Light Source-II (NSLS-II) project is now in the construction stage. A new insertion device (ID) magnetic measurement facility (MMF) is being set up at Brookhaven National Laboratory in order to satisfy the stringent requirement on the magnetic field measurement of IDs. ISO-Class7 temperature stabilized clean room is being constructed for this purpose. A state-of-the-art Hall probe bench and integrated field measurement system will be installed therein. IDs in the project baseline scope include six damping wigglers, two elliptically polarizing undulators (EPUs), three 3.0m long in-vacuum undulators (IVUs) and one 1.5m long IVU. Three-pole wigglers with peak field over 1 Tesla will be utilized to accommodate the users of bending magnet radiation at the NSLS. Future plans includes: (1) an in-vacuum magnetic measurement system, (2) use of PrFeB magnet for improved cryo undulator, (3) development of advanced optimization program for sorting and shimming of IDs, (4) development of a closed loop He gas refrigerator, (5) switchable quasi-periodic EPU. Design features of the baseline devices, IDMMF and the future plans for NSLS-II ID activities are described.

  9. [Application of depth-analysis of confocal Raman micro-spectroscopy to chirography identification].

    PubMed

    Lin, Hai-Bo; Xu, Xiao-Xuan; Wang, Bin; Yang, Yan-Yong; Yu, Gang; Zhang, Cun-Zhou; Li, Jie

    2005-01-01

    Depth analysis of confocal Raman micro-spectroscopy was applied to chirography identification. The result indicated that depth analysis has potential application to forensic science field, especially in longitudinal identification of ink and inkpad. No matter what the spatial distributions of the signature pen and inkpad are, confocal Raman micro-spectroscopy can longitudinally distinguish those spatial differences. All those suggested that confocal Raman micro-spectroscopy is a fast, simple, high sensitive and non-destructive technique.

  10. Brillouin microspectroscopy assessment of tissue differentiation during embryonic development

    NASA Astrophysics Data System (ADS)

    Troyanova-Wood, Maria; Meng, Zhaokai; Silverberg, Hannah; Yakovlev, Vladislav V.

    2017-02-01

    Changes in mechanical properties represent one of the driving factors behind cell differentiation during embryonic development. However, measuring these changes without disrupting the normal progression of morphogenesis or destroying the developing organism is not trivial. Brillouin microspectroscopy has been shown to be capable of nocontact, non-destructive and non-disruptive assessment of elastic properties in developing zebrafish embryos. The present study builds upon the previous work, and observes the changes in elasticity during the development of heart and brain in zebrafish embryos from 8 to 28 hpf (hours post-fertilization) at regular intervals. Brillouin microspectroscopy has proved to be a suitable technique to continuously monitor tissue differentiation and the development of individual organs with high spatial resolution without harming the developing organism.

  11. Orientation-distribution mapping of polycrystalline materials by Raman microspectroscopy

    PubMed Central

    Schmid, T.; Schäfer, N.; Levcenko, S.; Rissom, T.; Abou-Ras, D.

    2015-01-01

    Raman microspectroscopy provides the means to obtain local orientations on polycrystalline materials at the submicrometer level. The present work demonstrates how orientation-distribution maps composed of Raman intensity distributions can be acquired on large areas of several hundreds of square micrometers. A polycrystalline CuInSe2 thin film was used as a model system. The orientation distributions are evidenced by corresponding measurements using electron backscatter diffraction (EBSD) on the same identical specimen positions. The quantitative, local orientation information obtained by means of EBSD was used to calculate the theoretical Raman intensities for specific grain orientations, which agree well with the experimental values. The presented approach establishes new horizons for Raman microspectroscopy as a tool for quantitative, microstructural analysis at submicrometer resolution. PMID:26673970

  12. Probing axial orientation of collagen fibers with Brillouin microspectroscopy

    NASA Astrophysics Data System (ADS)

    Meng, Zhaokai; Yakovlev, Vladislav V.

    2015-03-01

    Collagen is an important structural component in many biological tissues including bone, teeth, skin, and vascular endothelial layer. Its fibrillar arrangement can produce tissues with distinct anisotropies and is responsible for its unique elastic properties. However, current methods of retrieving orientation of those fibers show low sensitivity to the out-of-plane orientations. In this report, we employed Brillouin microspectroscopy to probe the local sound velocity, which, in its turn, is found to have a strong correlation to the local fibrillar arrangements.

  13. Letter : NIR FT-Raman microspectroscopy of fluid inclusions: Comparisons with VIS Raman and FT-IR microspectroscopies

    NASA Astrophysics Data System (ADS)

    Pironon, J.; Sawatzki, J.; Dubessy, J.

    1991-12-01

    The first Raman spectra of hydrocarbon inclusions using Fourier transform (FT) Raman microspectroscopy were obtained with a 1064 nm laser excitation in the near-infrared range (NIR FT-Raman). Some inclusions reveal the typical CH vibrational bands of organic compounds, but most of the inclusions that are fluorescent during visible Raman microspectroscopy (514 nm excitation) are still fluorescent in the NIR range. These Raman spectra are presented and compared to the conventional visible (VIS) Raman and FT-IR spectra. For spectra obtained on the same nonfluorescent inclusion, the signal/background ratio is lower in NIR FT-Raman than in VIS Raman. This ratio should be improved by application of more sensitive detectors. The increase of the power density (laser power/impact laser area) could be a future improvement in the limit of thermal background excitation and pyrolysis of the oils trapped in inclusions.

  14. Measuring cellular-scale nutrient distribution in algal biofilms with synchrotron confocal infrared microspectroscopy

    USDA-ARS?s Scientific Manuscript database

    Infrared microspectroscopy (IMS) and chemical imaging is ideal for measuring nutrient distribution in single algal cells on a cellular and subcellular level. The study of small algal cells, or cells within a colony requires enhanced spatial resolution IMS. Synchrotron infrared microspectroscopy wit...

  15. Performance of the double multilayer monochromator on the NSLS wiggler beam line X25

    SciTech Connect

    Berman, Lonny E.; Yin Zhijian; Dierker, Steven B.; Dufresne, Eric; Mochrie, Simon G. J.; Tsui, Ophelia K. C.; Burley, Stephen K.; Shu Fong; Xie Xiaoling; Capel, Malcolm S.; Sweet, Robert M.

    1997-07-01

    A tunable, double multilayer x-ray monochromator has recently been implemented on the National Synchrotron Light Source (NSLS) X25 wiggler beam line. It is based on a parallel pair of tungsten-boron-carbide multilayer films grown on silicon substrates and purchased from Osmic, Inc. of Troy, Michigan, USA. It acts as an optional alternative to the conventional double silicon crystal monochromator, and uses the same alignment mechanism. Two other NSLS beam lines also have had this kind of monochromator installed recently, following the lead of the NSLS X20C IBM/MIT beam line which has used a double multilayer monochromator for several years. Owing to the 100 times broader bandwidth of a multilayer x-ray monochromator, compared with a silicon monochromator, the multilayer monochromator has the obvious advantage of delivering 100 times the flux of a silicon monochromator, and thereby makes more efficient use of the continuous synchrotron radiation spectrum, yet preserves the narrow collimation of the incident synchrotron beam. In particular, multilayer x-ray bandwidths, on the order of 1%, are well-matched to x-ray undulator linewidths. Performance results for the X25 multilayer monochromator are presented, comparing it with the silicon monochromator. Of note is its short- and long-term performance as an x-ray monochromator delivering the brightness of the wiggler source in the presence of the high-power white beam. Detailed measurements of its spatial beam profile and wavelength dispersion have been made, and it is shown how its resolution could be improved when desired. Finally, its peculiar, anisotropic resolution function in reciprocal space, and its bearing upon x-ray crystallography and scattering experiments, will be discussed, and highlighted by the results of a protein crystallography experiment.

  16. Operation of a small-gap undulator on the NSLS X-ray Ring

    SciTech Connect

    Stefan, P.M.; Krinsky, S.; Rakowsky, G.; Solomon, L.

    1995-02-01

    The authors report results of an on-going experiment being carried out in the X13 straight section of the NSLS X-ray Ring which explores the limits of the operation of small-gap undulators. In particular, they discuss the operation of a 16 mm period small-gap undulator. At an electron beam current of 300 mA the variable gap vacuum chamber has been closed to an inner aperture of 3.8 mm with no effect on the electron beam lifetime. Measurements of the output radiation spectrum at a magnet gap of 7.5 mm are described.

  17. Commissioning and Early Operation Experience of the NSLS-II Storage Ring RF System

    SciTech Connect

    Gao, F.; Rose, J.; Cupolo, J.; Dilgen, T.; Rose, B.; Gash, W.; Ravindranath, V.; Yeddulla, M.; Papu, J.; Davila, P.; Holub, B.; Tagger, J.; Sikora, R.; Ramirez, G.; Kulpin, J.

    2015-05-03

    The National Synchrotron Light Source II (NSLS-II) is a 3 GeV electron X-ray user facility commissioned in 2014. The storage ring RF system, essential for replenishing energy loss per turn of the electrons, consists of digital low level RF controllers, 310 kW CW klystron transmitters, CESR-B type superconducting cavities, as well as a supporting cryogenic system. Here we will report on RF commissioning and early operation experience of the system for beam current up to 200mA.

  18. On-axis microscopes for the inelastic x-ray scattering beamline at NSLS-II

    SciTech Connect

    Gofron, K. J. Cai, Y. Q.; Coburn, D. S.; Antonelli, S.; Suvorov, A.; Flores, J.

    2016-07-27

    A novel on-axis X-ray microscope with 3 µm resolution, 3x magnification, and a working distance of 600 mm for in-situ sample alignment and X-ray beam visualization for the Inelastic X-ray Scattering (IXS) beamline at NSLS-II is presented. The microscope uses reflective optics, which minimizes dispersion, and allows imaging from Ultraviolet (UV) to Infrared (IR) with specifically chosen objective components (coatings, etc.). Additionally, a portable high resolution X-ray microscope for KB mirror alignment and X-ray beam characterization was developed.

  19. X-324: An upgrade to the NSLS X-Ray Ring using B factory technology

    SciTech Connect

    Blum, E.B.

    1993-12-02

    Through much of the last decade, the NSLS has been America`s preeminent source of synchrotron radiation. In the near future, The NSLS will face formidable competition from the third generation light sources, designed to produce high brightness beams from undulators. Because of the lattice design of the NSLS rings and the limited number of straight sections for new undulators it will be impossible to compete with the new rings in brightness at short wavelengths. It is not clear, however, how many experiments really need brightness and how many just need flux. A good strategy could lie in keeping the NSLS the highest flux synchrotron light source in the country and leaving the brightness frontier to the third generation rings. By using the technology developed for the SLAC B factory we can simultaneously raise the X-Ray Ring energy to 3.0 GeV and the current to 2.4 Amp. From these parameters I am calling the proposed upgrade X-324. After the X-324 upgrade, the X-Ray Ring will produce twenty times more synchrotron radiation power than is produced by today`s 250 mA, 2.5 GeV beams. This is a qualitative change from today`s conditions and will place great demands on the RF and vacuum systems. The requirements are similar to those for the SLAC PEP-II B factory. PEP-II will have two rings, one at 3.1 GeV and the other at 9 GeV. The maximum design current in both rings is 3 Amp although the operating current will not be as large. The PEP-II design calls for high power, single cell, 476 MHz RF cavities and a cooper vacuum chamber to cope with the intense synchrotron radiation emitted. We can adapt these designs for X-324. In this paper I will be describing some estimates that I have made about certain aspects of the upgrade. I will not be presenting a complete design but I hope to show that more detailed planning is warranted.

  20. Overview of Beam Instrumentation and Diagnostics for the NSLS-II Project

    SciTech Connect

    Singh,O.

    2008-05-04

    A new, ultra-bright 3rd generation light source, the NSLS-II Project, is planned to be built at Brookhaven National Laboratory. The light source being developed will have unprecedently small beam horizontal emittance and will provide the radiation sources with a brightness of 3 x 10{sup 21} photons/sec/0.1%BW/mm{sup 2}/mrad{sup 2}. In this paper we present the detailed specifications and a comprehensive description of the planned beam instrumentation system and the first results of the ongoing instrumentation R&D activities on beyond state-of-the-art subsystems.

  1. Optical design and performance of the X25 hybrid wiggler beam line at the NSLS

    SciTech Connect

    Berman, L.E.; Hastings, J.B.; Oversluizen, T.; Woodle, M.

    1991-01-01

    The X25 beam line at the National Synchrotron Light Source (NSLS) began full-power commissioning in 1990. It extracts radiation from a 27 pole hybrid wiggler, which produces up to 1.8 kW of total power with a peak horizontal density of 450 W/mrad and critical energy of 4.6 keV. The design and performance of the beam line optics are described, in particular the cooling of the first monochromator crystal. 28 refs., 5 figs.

  2. NSLS 2003 ACTIVITY REPORT (NATIONAL SYNCHROTRON LIGHT SOURCE ACTIVITY REPORT 2003)

    SciTech Connect

    MILLER,L.

    2004-05-01

    The scientific productivity of the NSLS continues to be outstanding and the research conducted here has high impact. 2003 was no exception and some of the many highlights from this year's research activity are included in this Activity Report. We are especially pleased that one of our users, Professor Roderick MacKinnon (Rockefeller University), was the co-recipient of the 2003 Nobel Prize in Chemistry for work, much of which was done at the NSLS, explaining how proteins known as ion channels help to generate nerve impulses. It is also a particular pleasure to note that NSLS accelerator physicist Li Hua Yu was awarded the 2003 International Free Electron Laser Prize in recognition of his outstanding achievements, especially demonstrating High Gain Harmonic Generation (HGHG) at the DUV-FEL. Our vision for the NSLS in the next five to 10 years is for it to continue to serve as a vital resource for the nation and especially for the strong Northeast research community. To accomplish this, we are working to preserve and enhance its outstanding scientific productivity by providing increased user support and upgrading beamline and endstation instrumentation. For example, this past year we collaborated with scientists from the Albert Einstein College of Medicine and the BNL Biology Department to develop a new undulator beamline, X29, to meet the needs of macromolecular crystallography for high brightness x-rays. A new endstation on the undulator beamline X13B is being equipped with optics and instrumentation for microdiffraction and microprobe experiments. The wiggler beamline, X21, is being upgraded to provide high intensity and increased capacity for small angle x-ray scattering experiments on nanotemplated soft matter, biomaterials, and other systems. We are collaborating with the BNL Center for Functional Nanomaterials to develop a beamline for LEEM/PEEM studies, which will add important new capabilities for nanoscience and catalysis research. A new high-speed, high

  3. Operation of a small-gap undulator on the NSLS X-ray Ring

    SciTech Connect

    Stefan, P.M.; Krinsky, S.; Rakowsky, G.; Solomon, L.

    1995-01-01

    We report results of an on-going experiment being carried out in the X13 straight section of the NSLS X-ray Ring which explores the limits of the operation of small-gap undulators. In particular, we discuss the operation of a 16 mm period small-gap undulator. At an electron beam current of 300 mA the variable gap vacuum chamber has been closed to an inner aperture of 3.8 mm with no effect on the electron beam lifetime. Measurements of the output radiation spectrum at a magnet gap of 7.5 mm are described.

  4. Beam Based Calibration of Slow Orbit Bump in the NSLS Booster

    SciTech Connect

    Yang, X.; Shaftan, T.; Rose, J.

    2009-05-04

    The orbit bumps in NSLS booster are used to move the beam orbit within 2mm of the extraction septum aperture on a time scale of millisecond at extraction in order to reduce the requirement on the amplitude of the fast extraction kicker. This may cause charge losses since before extraction, the beam stays on the distorted orbit for thousands of revolutions. In order to find the optimal orbit bump setpoint, which brings the maximum distortion at the extraction position and minimum distortions everywhere else, we developed an extraction model and performed an experiment to validate it. Afterwards, the model was applied to optimize the extraction process.

  5. IMPEDANCE OF ELECTRON BEAM VACUUM CHAMBERS FOR THE NSLS-II STORAGE RING.

    SciTech Connect

    BLEDNYKH,A.; KRINSKY, S.

    2007-06-25

    In this paper we discuss computation of the coupling impedance of the vacuum chambers for the NSLS-II storage ring using the electromagnetic simulator GdfidL [1]. The impedance of the vacuum chambers depends on the geometric dimensions of the cross-section and height of the slot in the chamber wall. Of particular concern is the complex geometry of the infrared extraction chambers to be installed in special large-gap dipole magnets. In this case, wakefields are generated due to tapered transitions and large vertical-aperture ports with mirrors near the electron beam.

  6. COUPLING IMPEDANCE OF CESR-B RF CAVITY FOR THE NSLS-II STORAGE RING.

    SciTech Connect

    BLEDNYKH,A.; KRINSKY, S.; ROSE, J.

    2007-06-25

    CESR-B type superconducting cavities are under consideration for acceleration of the electron beam in the 3GeV NSLS-II storage ring. In this paper we present detailed investigation of longitudinal and transverse impedance of CESR-B cavity and transitions. Ferrite material is included in impedance analysis. Its effect on short range wake potential has been studied using GdfidL code. The summary results of loss factors and kick factors are presented for a 3mm rms bunch length.

  7. Global DC closed orbit correction experiment on the NSLS x-ray ring

    SciTech Connect

    Chung, Y.; Decker, G.; Evans, K.

    1992-09-15

    In this note are described the global DC closed orbit correction experiments conducted on the X-ray ring at National Synchrotron Light Source (NSLS). The beam response matrix, defined as beam motion at BPM locations per unit kick by corrector magnets, was measured and then inverted using the technique of singular value decomposition (SVD). The product of the inverted matrix and the difference orbit gives the incremental kick strengths necessary to correct the orbit. As a result, the r.m.s. orbit error around the ring was reduced from 208 {mu}m to 61 {mu}m.

  8. Evidence for millimeter-wave coherent emission from the NSLS VUV ring

    SciTech Connect

    Carr, G.L.

    1999-07-19

    Coherent synchrotron radiation from the NSLS VUV ring has been detected and partially characterized. The observations have been performed at the new far infrared beamline U12IR. The coherent radiation is peaked near a wavelength of 7mm and occurs in short duration bursts. The bursts occur only when the electron beam current (I) exceeds a threshold value (I{sub th}), which itself varies with ring operating conditions. Beyond threshold, the average intensity of the emission is found to increase as (I-I{sub th}). The coherent emission implies micro-bunching of the electron beam due to a longitudinal instability.

  9. EVIDENCE FOR MILLIMETER-WAVE COHERENT EMISSION FROM THE NSLS VUV RING.

    SciTech Connect

    CARR,G.L.

    1999-07-19

    Coherent synchrotron radiation from the NSLS VUV ring has been detected and partially characterized. The observations have been performed at the new far infrared beamline U12IR. The coherent radiation is peaked near a wavelength of 7mm and occurs in short duration bursts. The bursts occur only when the electron beam current (I) exceeds a threshold value (I{sub th}), which itself varies with ring operating conditions. Beyond threshold, the average intensity of the emission is found to increase as (I-I{sub th}). The coherent emission implies micro-bunching of the electron beam due to a longitudinal instability.

  10. Safe operating conditions for NSLS-II Storage Ring Frontends commissioning

    SciTech Connect

    Seletskiy, S.; Amundsen, C.; Ha, K.; Hussein, A.

    2015-04-02

    The NSLS-II Storage Ring Frontends are designed to safely accept the synchrotron radiation fan produced by respective insertion device when the electron beam orbit through the ID is locked inside the predefined Active Interlock Envelope. The Active Interlock is getting enabled at a particular beam current known as AI safe current limit. Below such current the beam orbit can be anywhere within the limits of the SR beam acceptance. During the FE commissioning the beam orbit is getting intentionally disturbed in the particular ID. In this paper we explore safe operating conditions for the Frontends commissioning.

  11. COMPARISON OF DOUBLE BEND AND TRIPLE BEND ACHROMATIC LATTICE STRUCTURES AND NSLS-II.

    SciTech Connect

    KRAMER, S.L.; KRINSKY, S.; BENGTSSON, J.

    2006-06-26

    The Double Bend Achromatic (DBA) and the Triple Bend Achromatic (TBA) lattice have been studied rather extensively for use for the NSLS-II storage ring. The advantage of the TBA compared to the DBA in terms of emittance per period is well known. However, the DBA has the advantage of greater number of ID straight sections for the users and maybe easier to tune the dispersive section for reduced chromatic sextupole strength. We present a comparison of these lattices based on optimization of the non-linear driving terms using high order achromatic cancellation of driving terms of the nonlinear lattice.

  12. Background-Free Nonlinear Microspectroscopy with Vibrational Molecular Interferometry

    PubMed Central

    Garbacik, Erik T.; Korterik, Jeroen P.; Otto, Cees; Mukamel, Shaul; Herek, Jennifer L.; Offerhaus, Herman L.

    2013-01-01

    We demonstrate a method for performing nonlinear microspectroscopy that provides an intuitive and unified description of the various signal contributions, and allows the direct extraction of the vibrational response. Three optical fields create a pair of Stokes Raman pathways that interfere in the same vibrational state. Frequency modulating one of the fields leads to amplitude modulations on all of the fields. This vibrational molecular interferometry technique allows imaging at high speed free of nonresonant background, and is able to distinguish between electronic and vibrational contributions to the total signal. PMID:22243075

  13. Cellular injury evidenced by impedance technology and infrared microspectroscopy

    NASA Astrophysics Data System (ADS)

    le Roux, K.; Prinsloo, L. C.; Meyer, D.

    2015-03-01

    Fourier Transform Infrared (FTIR) spectroscopy is finding increasing biological application, for example in the analysis of diseased tissues and cells, cell cycle studies and investigating the mechanisms of action of anticancer drugs. Cancer treatment studies routinely define the types of cell-drug responses as either total cell destruction by the drug (all cells die), moderate damage (cell deterioration where some cells survive) or reversible cell cycle arrest (cytostasis). In this study the loss of viability and related chemical stress experienced by cells treated with the medicinal plant, Plectranthus ciliatus, was investigated using real time cell electronic sensing (RT-CES) technology and FTIR microspectroscopy. The use of plants as medicines is well established and ethnobotany has proven that crude extracts can serve as treatments against various ailments. The aim of this study was to determine whether FTIR microspectroscopy would successfully distinguish between different types of cellular injury induced by a potentially anticancerous plant extract. Cervical adenocarcinoma (HeLa) cells were treated with a crude extract of Pciliatus and cells monitored using RT-CES to characterize the type of cellular responses induced. Cell populations were then investigated using FTIR microspectroscopy and statistically analysed using One-way Analysis of Variance (ANOVA) and Principal Component Analysis (PCA). The plant extract and a cancer drug control (actinomycin D) induced concentration dependent cellular responses ranging from nontoxic, cytostatic or cytotoxic. Thirteen spectral peaks (915 cm-1, 933 cm-1, 989 cm-1, 1192 cm-1, 1369 cm-1, 1437 cm-1, 1450 cm-1, 1546 cm-1, 1634 cm-1, 1679 cm-1 1772 cm-1, 2874 cm-1 and 2962 cm-1) associated with cytotoxicity were significantly (p value < 0.05, one way ANOVA, Tukey test, Bonferroni) altered, while two of the bands were also indicative of early stress related responses. In PCA, poor separation between nontoxic and cytostatic

  14. Background-free nonlinear microspectroscopy with vibrational molecular interferometry

    NASA Astrophysics Data System (ADS)

    Garbacik, Erik T.; Korterik, Jeroen P.; Otto, Cees; Mukamel, Shaul; Herek, Jennifer L.; Offerhaus, Herman L.

    2012-03-01

    We demonstrate a method for performing nonlinear microspectroscopy that provides an intuitive and unified description of the various signal contributions, and allows the direct extraction of the vibrational response. Three optical fields create a pair of Stokes Raman pathways that interfere in the same vibrational state. Frequency modulating one of the fields leads to amplitude modulations on all of the fields. This vibrational molecular interferometry (VMI) technique allows imaging at high speed free of non-resonant background, and is able to distinguish between electronic and vibrational contributions to the total signal.

  15. Vibrational Micro-Spectroscopy of Human Tissues Analysis: Review.

    PubMed

    Bunaciu, Andrei A; Hoang, Vu Dang; Aboul-Enein, Hassan Y

    2017-05-04

    Vibrational spectroscopy (Infrared (IR) and Raman) and, in particular, micro-spectroscopy and micro-spectroscopic imaging have been used to characterize developmental changes in tissues, to monitor these changes in cell cultures and to detect disease and drug-induced modifications. The conventional methods for biochemical and histophatological tissue characterization necessitate complex and "time-consuming" sample manipulations and the results are rarely quantifiable. The spectroscopy of molecular vibrations using mid-IR or Raman techniques has been applied to samples of human tissue. This article reviews the application of these vibrational spectroscopic techniques for analysis of biological tissue published between 2005 and 2015.

  16. Ultrasonic Microspectroscopy Measurement of Fictive Temperature for Synthetic Silica Glass

    NASA Astrophysics Data System (ADS)

    Kushibiki, Jun-ichi; Arakawa, Mototaka; Ohashi, Yuji; Maruyama, Yuko

    2011-05-01

    Experimental procedures to evaluate the fictive temperature (TF) of synthetic silica glass were developed using ultrasonic microspectroscopy (UMS) technology by measuring longitudinal-wave velocity (Vl). Two kinds of commercial synthetic silica glass (without and with water) were demonstrated, resulting in the establishment of calibration lines between Vl and TF with a resolution within 1 °C and clear observation of their hydroxyl (OH) dependences. This ultrasonic method and system will be extremely useful and effective for improving mass-production conditions of glass ingots as well as for conducting basic studies on glass science.

  17. Improving sensitivity in nonlinear Raman microspectroscopy imaging and sensing

    PubMed Central

    Arora, Rajan; Petrov, Georgi I.; Liu, Jian; Yakovlev, Vladislav V.

    2011-01-01

    Nonlinear Raman microspectroscopy based on a broadband coherent anti-Stokes Raman scattering is an emerging technique for noninvasive, chemically specific, microscopic analysis of tissues and large population of cells and particles. The sensitivity of this imaging is a critical aspect of a number of the proposed biomedical application. It is shown that the incident laser power is the major parameter controlling this sensitivity. By careful optimizing the laser system, the high-quality vibrational spectra acquisition at the multi-kHz rate becomes feasible. PMID:21361677

  18. Crack analysis of unfilled natural rubber using infrared microspectroscopy

    SciTech Connect

    Neumeister, L.A.; Koenig, J.L.

    1996-10-01

    The characterization and analysis of the crack tip region in unfilled natural rubber is crucial in developing a fatigue resistant material. Therefore, the molecular structure and orientation of the material in the crack tip region has been compared to the bulk. Cracks formed by different methods were evaluated using both transmission and reflection techniques of infrared microspectroscopy. The material around the crack tip and edges shows much higher absorbances than the bulk material for stressed rubber. This is due to more material and predominantly, from residual orientation effects. For unstressed material the crack tip region exhibits identical characteristics to the bulk material.

  19. Latest experiences and future plans on NSLS-II insertion devices

    SciTech Connect

    Tanabe, T.; Hidaka, Y.; Kitegi, C.; Hidas, D.; Musardo, M.; Harder, D. A.; Rank, J.; Cappadoro, P.; Fernandes, H.; Corwin, T.

    2016-07-27

    National Synchrotron Light Source-II (NSLS-II) is the latest storage ring of 3 GeV energy at the Brookhaven National Laboratory (BNL). The horizontal emittance of the electron beam with the currently installed six damping wigglers is 0.9 nm.rad, which could be further reduced to 0.5 nm.rad with more insertion devices (IDs). With only one RF cavity the beam current is restricted to 200 mA. Five hundred mA operation is envisaged for next year with an addition of the second cavity. Six (plus two branches) beamlines have been commissioned in the initial phase of the project. In July 2015, three NIH funded beamlines called “Advanced Beamlines for Biological Investigations with X-rays” (ABBIX) will be added for operation. This paper describes the experiences of ID development, installation, and commissioning for the NSLS-II project as well as our future plans to improve the performance of the facility in terms of source development.

  20. DESIGN AND PRELIMINARY TEST OF THE 1500 MHZ NSLS-II PASSIVE SUPERCONDUCTING RF CAVITY

    SciTech Connect

    Rose, J.; Gash, W.; Kosciuk, B.; Ravindranath, V.; Sikora, B.; Sharma, S.; Towne, N.; Grimm, T.L.; Boulware, C.H.; Krizmanich, C.; Kuhlman, B.; Miller, N.; Siegel, B.; Winowski, M.

    2011-03-28

    NSLS-II is a new ultra-bright 3 GeV 3rd generation synchrotron radiation light source. The performance goals require operation with a beam current of 500mA and a bunch current of at least 0.5mA. Ion clearing gaps are required to suppress ion effects on the beam. The natural bunch length of 3mm is planned to be lengthened by means of a third harmonic cavity in order to increase the Touschek limited lifetime. Earlier work described the design alternatives and the geometry selected for a copper prototype. We subsequently have iterated the design to lower the R/Q of the cavity and to increase the diameter of the beam pipe ferrite HOM dampers to reduce the wakefield heating. A niobium cavity and full cryomodule including LN2 shield, magnetic shield and insulating vacuum vessel have been fabricated and installed. A passive SRF 3rd harmonic cavity consisting of two tightly coupled cells has been designed and fabricated for NSLS-II. Initial cold tests of this cavity are very promising. These tests have verified that the cavity frequency and mode separation between the 0 and {pi}-modes can be set at manufacture. Further, the frequency separation can be maintained over wide tuning ranges necessary for operation. Future work includes HOM damper and motorized tuner development.

  1. LOW HORIZONTAL BETA FUNCTION IN LONG STRAIGHTS OF THE NSLS-II LATTICE

    SciTech Connect

    Fanglei, L.; Bengtsson, J.; Guo, W.; Krinsky, S.; Li, Y.; Yang, L.

    2011-03-28

    The NSLS-II storage ring lattice is comprised of 30 DBA cells arranged in 15 superperiods. There are 15 long straight sections (9.3m) for injection, RF and insertion devices and 15 short straights (6.6m) for insertion devices. In the baseline lattice, the short straights have small horizontal and vertical beta functions but the long straights have large horizontal beta function optimized for injection. In this paper, we explore the possibility of maintaining three long straights with large horizontal beta function while providing the other 12 long straights with smaller horizontal beta function to optimize the brightness of insertion devices. Our study considers the possible linear lattice solutions as well as characterizing the nonlinear dynamics. Results are reported on optimization of dynamic aperture required for good injection efficiency and adequate Touschek lifetime. This paper discusses dynamic aperture optimization for the NSLS-II lattice with alternate high and low horizontal beta function in the long straights, which is proposed for the optimization of the brightness of insertion devices. The linear optics is optimized to meet the requirements of lattice function and source properties. Nonlinear optimization for a lattice with working point at (37.18, 16.2) is performed. Considering the realistic magnets errors and physical apertures, we calculate the frequency maps and plot the tune footprint. The results show that the lattice with high-low beta function has adequate dynamic aperture for good injection efficiency and sufficient Touschek lifetime.

  2. Design of the NSLS-II Linac Front End Test Stand

    SciTech Connect

    Fliller III, R.; Johanson, M.; Lucas, M.; Rose, J.; Shaftan, T.

    2011-03-28

    The NSLS-II operational parameters place very stringent requirements on the injection system. Among these are the charge per bunch train at low emittance that is required from the linac along with the uniformity of the charge per bunch along the train. The NSLS-II linac is a 200 MeV linac produced by Research Instruments Gmbh. Part of the strategy for understanding to operation of the injectors is to test the front end of the linac prior to its installation in the facility. The linac front end consists of a 100 kV electron gun, 500 MHz subharmonic prebuncher, focusing solenoids and a suite of diagnostics. The diagnostics in the front end need to be supplemented with an additional suite of diagnostics to fully characterize the beam. In this paper we discuss the design of a test stand to measure the various properties of the beam generated from this section. In particular, the test stand will measure the charge, transverse emittance, energy, energy spread, and bunching performance of the linac front end under all operating conditions of the front end.

  3. A MODEL STUDY OF TRANSVERSE MODE COUPLING INSTABILITY AT NATIONAL SYNCHROTRON LIGHT SOURCE-II (NSLS-II).

    SciTech Connect

    BLEDNYKH, A.; WANG, J.M.

    2005-05-15

    The vertical impedances of the preliminary designs of National Synchrotron Light Source II (NSLS-II) Mini Gap Undulators (MGU) are calculated by means of GdfidL code. The Transverse Mode Coupling Instability (TMCI) thresholds corresponding to these impedances are estimated using an analytically solvable model.

  4. Laser Microperforated Biodegradable Microbial Polyhydroxyalkanoate Substrates for Tissue Repair Strategies: An Infrared Microspectroscopy Studey

    SciTech Connect

    G Ellis; P Cano; M Jadraque; M Martin; L Lopez; T Nunez; E de la Pena; C Marco; L Garrido

    2011-12-31

    Flexible and biodegradable film substrates prepared by solvent casting from poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBHV) solutions in chloroform were microperforated by ultraviolet laser ablation and subsequently characterized using infrared (IR) microspectroscopy and imaging techniques and scanning electron microscopy (SEM). Both transmission synchrotron IR microspectroscopy and attenuated total reflectance microspectroscopy measurements demonstrate variations in the polymer at the ablated pore rims, including evidence for changes in chemical structure and crystallinity. SEM results on microperforated PHBHV substrates after cell culture demonstrated that the physical and chemical changes observed in the biomaterial did not hinder cell migration through the pores.

  5. High-throughput vibrational cytometry based on nonlinear Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Arora, R.; Petrov, G. I.; Yakovlev, V. V.

    2010-02-01

    Flow cytometry is a technology that allows a single cell or particle to be measured for a variety of characteristics, determined by looking at their properties while they flow in a liquid stream. High speed of flow and huge number of objects to be analyzed imposed some strict criteria on which methods can be used for analysis. All the known commercial instruments are currently using light scattering for particle sizing and fluorescence detection for chemical recognition. However, vibrational spectroscopy is the only non-invasive optical spectroscopy tool, which has proven to provide chemically-specific information about the interrogated sample. It is proposed that vibrational spectroscopy, based on nonlinear Raman scattering can be used to serve as an analytical tool for cytometry by providing rapid and accurate chemical recognition of flowing materials. To achieve a desired speed (>10,000 cell/particles per second), we have substantially upgraded our previous system for nonlinear Raman microspectroscopy. By increasing the size of the excitation volume to the size of a cell and by keeping the incident intensity at the same level, a dramatic increase of the nonlinear Raman signal is achieved. This allows high-quality vibrational spectra to be acquired within 10-100 microsecond from a single yeast cell without any observable damage to the irradiated cell. This is four orders of magnitude better than any previous attempts involving Raman microspectroscopy.

  6. In situ high-temperature visible microspectroscopy for volcanic materials.

    PubMed

    Yamanoi, Yuta; Nakashima, Satoru

    2005-11-01

    In situ high-temperature visible microspectroscopy has been developed in order to study color change kinetics of volcanic materials. Olivine thin sections put on a synthetic alumina plate are heated on a heating stage at 600-800 degrees C under a visible microspectroscope. Changes in visible absorption spectra are monitored every 60 s for 5 hours. The obtained high-temperature visible spectra showed a gradual increase with time in absorbance in the shorter wavelength region (400-600 nm). The 430 nm absorbance (ligand field transition of Fe3+ increased more with time at higher temperatures. Assuming diffusional transport in plane sheets, apparent diffusion coefficients were determined at temperatures of 600-800 degrees C. The activation energy for this diffusion in olivine is 208 +/- 17 kJ/mol. This activation energy value is similar to those for the metal vacancy diffusion in olivine. This newly developed in situ high-temperature visible microspectroscopy can provide kinetic measurements of visible spectral change of materials at high temperatures such as volcanic materials.

  7. Biomedical applications of the ESRF synchrotron-based microspectroscopy platform.

    PubMed

    Bohic, S; Cotte, M; Salomé, M; Fayard, B; Kuehbacher, M; Cloetens, P; Martinez-Criado, G; Tucoulou, R; Susini, J

    2012-02-01

    Very little is known about the sub-cellular distribution of metal ions in cells. Some metals such as zinc, copper and iron are essential and play an important role in the cell metabolism. Dysfunctions in this delicate housekeeping may be at the origin of major diseases. There is also a prevalent use of metals in a wide range of diagnostic agents and drugs for the diagnosis or treatment of a variety of disorders. This is becoming more and more of a concern in the field of nanomedicine with the increasing development and use of nanoparticles, which are suspected of causing adverse effects on cells and organ tissues. Synchrotron-based X-ray and Fourier-transformed infrared microspectroscopies are developing into well-suited sub-micrometer analytical tools for addressing new problems when studying the role of metals in biology. As a complementary tool to optical and electron microscopes, developments and studies have demonstrated the unique capabilities of multi-keV microscopy: namely, an ultra-low detection limit, large penetration depth, chemical sensitivity and three-dimensional imaging capabilities. More recently, the capabilities have been extended towards sub-100nm lateral resolutions, thus enabling sub-cellular chemical imaging. Possibilities offered by these techniques in the biomedical field are described through examples of applications performed at the ESRF synchrotron-based microspectroscopy platform (ID21 and ID22 beamlines).

  8. Phenotypic Expression in Wheat Revealed Using FT-IR Microspectroscopy

    SciTech Connect

    Brewer, L.; Wetzel, D

    2009-01-01

    Wheat selected for cultivation through the centuries has a glume that is 'soft' instead of 'tough' as naturally occurring. In production, this is desirable because it enables mechanical threshing with efficient separation of kernel from the head of each stalk without damaging the kernel. FT-IR microspectroscopy provides chemically based, objective assessment of genetic expression by measuring the extent of genetic expression. In the Microbeam Molecular Spectroscopy Laboratory, Manhattan, KS, an imaging FT-IR microspectrometer with a detector array focused on the image plane was used to obtain spectral data from dissected glume specimens of nine tough and eleven soft wheat cultivars in a rectangular mapping pattern. With cellulose as the substrate, the extent of lignification is measurable from the ratio of the lignin (1508 cm{sup -1}) baseline adjusted band area to the representative cellulosic (1370 cm{sup -1}) band area. A distinction between soft and tough glumes is obtained in numerical terms. Using a band ratio minimizes variation due to thickness differences. While analyzing mapped sections of glume, care is taken to avoid tabulation of spectral data from vascular bundles. Inclusion of these data would to avoid tabulation of spectral data from vascular bundles. Inclusion of these data would bias the analysis toward the composition of highly lignified vascular bundles. Spatially resolved focal plane array FT-IR microspectroscopy reveals the extent of glume lignification that is coincident with the toughness trait. This enables breeders to rank the degree of lignin expression and discriminate between soft and tough breeding results.

  9. Characterization of Carbonaceous Material from the Sudbury Impact Structure Using Raman Microspectroscopy

    NASA Astrophysics Data System (ADS)

    Wright, A. J.; Parnell, J.; Ames, D. E.

    2008-03-01

    Samples from the 1.85 Ga Sudbury impact structure have been analyzed using Raman microspectroscopy in order to characterize the carbonaceous material and to investigate the relationship between the carbonaceous strata associated with the structure.

  10. Identification of Cortex Eucommiae from different producing areas by FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Sheng, Daping; Zhu, Zhengjie; Xu, Fangcheng; Huang, Dake; Yu, Changjun

    2015-04-01

    In this paper, FTIR microspectroscopy was used to compare Cortex Eucommiae from Anhui Province (A), Henan Province (B) and Sichuan Province (C) of China. High-resolution spectra were obtained with good reproducibility. From IR spectra, some obvious differences in band frequency could be observed among Cortex Eucommiae A-C. Curve fitting result indicated that polysaccharides' structures and contents were different among Cortex Eucommiae A-C. To distinguish Cortex Eucommiae from different producing areas, the A1245/A1328 ratio might be an exceptionally practical factor. Additionally, FTIR microspectroscopy could identify Cortex Eucommiae A-C with 89.5% accuracy in combination with hierarchical cluster analysis. The results suggest FTIR microspectroscopy is very easy and efficient for distinguishing Cortex Eucommiae from different areas, and also indicate FTIR microspectroscopy may be practical for TCM research.

  11. Another treatment of fluorescence polarization microspectroscopy and imaging.

    PubMed

    Fisz, Jacek J

    2009-04-16

    We here discuss a general (symmetry adapted) treatment for one-photon-excitation time-resolved fluorescence polarization microspectroscopy (TRFPM) at combined wide-angular excitation and detection apertures that correctly couples the principles of the optics of objective lenses with the principles of fluorescence spectroscopy with polarized light. The treatment is unified in the sense that it covers the electromagnetic description of focusing a linearly polarized beam of exciting light (diffraction theory, DT) and the description of the same problem in terms of the meridional plane properties (MPP) of the objective lenses (geometrical optics). It is shown that both approaches are quantitatively equivalent from the point of view of the polarization effects in typical TRFPM experiments on linear absorbers, despite the fact that in the MPP treatment the region of focus is treated as a pointlike object, while in the DT method the region of focus is characterized by a three-dimensional (3D) inhomogeneous electromagnetic field distribution, of generally ellipsoidal polarization at different points of the focus. This finding is essentially important from the point of view of the experimental practice because the MPP treatment is based on two very simple trigonometric expressions, in evident contrast to the DT method, in which the high-aperture focusing is described in terms of three complicated 3D integrals involving the Bessel functions of the first kind. A few words of comment are added on a similar problem in the case of nonlinear one-photon absorbers (e.g., chiral fluorophores). We discuss the synthetic fluorescence decays for the wide-field- and evanescent-wave-excitation confocal (or wide-field) detection fluorescence polarization microspectroscopy and imaging, which indicate the right experimental protocols for the kinetic and dynamic fluorescence polarization microspectroscopic studies. The manifestations of the effects resulting from the application of the wide

  12. FTIR-Microspectroscopy of Prion-Infected Nervous Tissue

    SciTech Connect

    Kretlow,A.; Wang, Q.; Kneipp, J.; Lasch, P.; Beekes, M.; Miller, L.; Naumann, D.

    2006-01-01

    The family of transmissible spongiform encephalopathies (TSE), also termed prion diseases, is a group of fatal, neurodegenerative diseases characterized by the accumulation of a misfolded protein, the disease-associated prion protein PrPSc. This glycoprotein differs in secondary structure from its normal, cellular isoform PrPC, which is physiologically expressed mostly by neurons. Scrapie is a prion disease first described in the 18th century in sheep and goats, and has been established as a model in rodents to study the pathogenesis and pathology of prion diseases. Assuming a multitude of molecular parameters change in the tissue in the course of the disease, FTIR microspectroscopy has been proposed as a valuable new method to study and identify prion-affected tissues due to its ability to detect a variety of changes in molecular structure and composition simultaneously. This paper reviews and discusses results from previous FTIR microspectroscopic studies on nervous tissue of scrapie-infected hamsters in the context of histological and molecular alterations known from conventional pathogenesis studies. In particular, data from studies reporting on disease-specific changes of protein structure characteristics, and also results of a recent study on hamster dorsal root ganglia (DRG) are discussed. These data include an illustration on how the application of a brilliant IR synchrotron light source enables the in situ investigation of localized changes in protein structure and composition in nervous cells or tissue due to PrPSc deposition, and a demonstration on how the IR spectral information can be correlated with results of complementary studies using immunohistochemistry and x-ray fluorescence techniques. Using IR microspectroscopy, some neurons exhibited a high accumulation of disease-associated prion protein evidenced by an increased amount of beta-sheet at narrow regions in or around the infected nervous cells. However, not all neurons from terminally diseased

  13. Industrial applications of accelerator-based infrared sources: Analysis using infrared microspectroscopy

    SciTech Connect

    Bantignies, J.L.; Fuchs, G.; Wilhelm, C.; Carr, G.L.; Dumas, P.

    1997-09-01

    Infrared Microspectroscopy, using a globar source, is now widely employed in the industrial environment, for the analysis of various materials. Since synchrotron radiation is a much brighter source, an enhancement of an order of magnitude in lateral resolution can be achieved. Thus, the combination of IR microspectroscopy and synchrotron radiation provides a powerful tool enabling sample regions only few microns size to be studied. This opens up the potential for analyzing small particles. Some examples for hair, bitumen and polymer are presented.

  14. Transmission-mode diamond white-beam position monitor at NSLS

    PubMed Central

    Muller, Erik M.; Smedley, John; Bohon, Jen; Yang, Xi; Gaowei, Mengjia; Skinner, John; De Geronimo, Gianluigi; Sullivan, Michael; Allaire, Marc; Keister, Jeffrey W.; Berman, Lonny; Héroux, Annie

    2012-01-01

    Two transmission-mode diamond X-ray beam position monitors installed at National Synchrotron Light Source (NSLS) beamline X25 are described. Each diamond beam position monitor is constructed around two horizontally tiled electronic-grade (p.p.b. nitrogen impurity) single-crystal (001) CVD synthetic diamonds. The position, angle and flux of the white X-ray beam can be monitored in real time with a position resolution of 500 nm in the horizontal direction and 100 nm in the vertical direction for a 3 mm × 1 mm beam. The first diamond beam position monitor has been in operation in the white beam for more than one year without any observable degradation in performance. The installation of a second, more compact, diamond beam position monitor followed about six months later, adding the ability to measure the angular trajectory of the photon beam. PMID:22514173

  15. Development and commissioning of an x-ray beam alignment flag for NSLS-II

    SciTech Connect

    Kosciuk, B. Hu, Y.; Keister, J.; Seletskiy, S.

    2016-07-27

    The NSLS-II Synchrotron Light Source is a 3 GeV electron storage ring recently commissioned and is now entering operations at Brookhaven National Laboratory. One of the major tasks was to commission the six project beamline front ends which required a diagnostic to resolve x-ray beam position for the purpose of beam alignment at low current. Since none of the front ends were outfitted with any x-ray diagnostics in the baseline design, an x-ray beam profile monitor or “flag” that could be easily installed into existing front end vacuum chambers was proposed to satisfy this requirement. Here we present the development of this novel device which utilizes a polycrystalline CVD diamond luminescent screen to produce a visible image of the x-ray beam cross-section and is then captured with a CCD camera.

  16. Transmission-mode diamond white-beam position monitor at NSLS.

    PubMed

    Muller, Erik M; Smedley, John; Bohon, Jen; Yang, Xi; Gaowei, Mengjia; Skinner, John; De Geronimo, Gianluigi; Sullivan, Michael; Allaire, Marc; Keister, Jeffrey W; Berman, Lonny; Héroux, Annie

    2012-05-01

    Two transmission-mode diamond X-ray beam position monitors installed at National Synchrotron Light Source (NSLS) beamline X25 are described. Each diamond beam position monitor is constructed around two horizontally tiled electronic-grade (p.p.b. nitrogen impurity) single-crystal (001) CVD synthetic diamonds. The position, angle and flux of the white X-ray beam can be monitored in real time with a position resolution of 500 nm in the horizontal direction and 100 nm in the vertical direction for a 3 mm × 1 mm beam. The first diamond beam position monitor has been in operation in the white beam for more than one year without any observable degradation in performance. The installation of a second, more compact, diamond beam position monitor followed about six months later, adding the ability to measure the angular trajectory of the photon beam.

  17. Transmission-mode diamond white-beam position monitor at NSLS

    SciTech Connect

    Muller E. M.; Heroux A.; Smedley, J.; Bohon, J.; Yang, X.; Gaowei, M.; Skinner, J.; De Geronimo, G.; Sullivan, M.; Allaire, M.; Keister, J. W.; Berman, L.

    2012-05-01

    Two transmission-mode diamond X-ray beam position monitors installed at National Synchrotron Light Source (NSLS) beamline X25 are described. Each diamond beam position monitor is constructed around two horizontally tiled electronic-grade (p.p.b. nitrogen impurity) single-crystal (001) CVD synthetic diamonds. The position, angle and flux of the white X-ray beam can be monitored in real time with a position resolution of 500 nm in the horizontal direction and 100 nm in the vertical direction for a 3 mm x 1 mm beam. The first diamond beam position monitor has been in operation in the white beam for more than one year without any observable degradation in performance. The installation of a second, more compact, diamond beam position monitor followed about six months later, adding the ability to measure the angular trajectory of the photon beam.

  18. MAGNETIC MEASUREMENT SYSTEM FOR THE NSLS SUPERCONDUCTING UNDULATOR VERTICAL TEST FACILITY.

    SciTech Connect

    HARDER, D.; CHOUHAN, S.; LEHECKA, M.; RAKOWSKY, G.; SKARITKA, J.; TANABE, T.

    2005-05-16

    One of the challenges of small-gap superconducting undulators is measurement of magnetic fields within the cold bore to characterize the device performance and to determine magnetic field errors for correction or shimming, as is done for room-temperature undulators. Both detailed field maps and integrated field measurements are required. This paper describes a 6-element, cryogenic Hall probe field mapper for the NSLS superconducting undulator Vertical Test Facility (VTF) [1]. The probe is designed to work in an aperture only 3 mm high. A pulsed-wire insert is also being developed, for visualization of the trajectory, for locating steering errors and for determining integrated multi-pole errors. The pulsed-wire insert will be interchangeable with the Hall probe mapper. The VTF and the magnetic measurement systems can accommodate undulators up to 0.4 m in length.

  19. AN OPTIMIZED DESIGN FOR THE NSLS 53 MHZ RF CAVITIES AND THE ANCILLARY COMPONENTS.

    SciTech Connect

    MORTAZAVI,P.

    2002-09-05

    RF cavities are among the most complex components of a particle accelerator. They perform optimally when all electrical, mechanical and vacuum requirements are fully integrated. This paper focuses on the mechanical design features of the new 53MHz room-temperature RF cavities (including their ancillary components) for the X-ray Ring at the National Synchrotron Light Source (NSLS). Differences between the new and previous designs of the RF cavities, input couplers, Higher-Order-Mode (HOM) dampers, and cooling and vacuum systems are reviewed. Thus far, two out of four units have already been constructed, tested, and installed into the X-Ray ring, and two additional RF cavities are planned. The features incorporated into the new all-copper RF cavities have already demonstrated superior performance over the original copper-plated steel design. The operating performance results along with some of manufacturing challenges are presented.

  20. Performance of a rapid-scan vacuum Michelson interferometer at the NSLS

    NASA Astrophysics Data System (ADS)

    Brierley, P.; Badeau, B.; Dumas, P.; Smith, M.; Williams, G. P.

    2002-03-01

    A commercial Nicolet Magna-IR series rapid-scan Michelson Fourier transform infrared was installed in a vacuum housing and integrated into the U4IR beamline at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory. The frequency reference laser was mounted outside the vacuum, but the moving mirror mechanism and the dynamic alignment system for the fixed mirror were in a vacuum. The performance of the instrument was measured in the usual way by measuring the repeatability of data collected under specific conditions of aperture, resolution, and mirror scanning velocity. We briefly discuss the beamline design, to put the interferometer in context, then present signal to noise data which we discuss in terms of both instrument performance and also storage ring beam stability. Under optimal conditions, the instrument has a reproducibility of 0.01% in 1 min of measuring time at a resolution of 2 cm-1, over a range from 100-3000 cm-1.

  1. Instabilities related with RF cavity in the booster synchrotron for NSLS-II

    SciTech Connect

    Kawashima, Y.; Cupolo, J.; Ma, H.; Oliva, J.; Rose, J.; Sikora, R.; Yeddulla, M.

    2010-12-01

    The booster synchrotron for NSLS-II accepts beam with 200 MeV from a linac and raises its energy up to 3 GeV. In order to raise beam energy up to 3 GeV, a 7-cell PETRA cavity is installed. Beam instabilities related to the cavity impedances are discussed. In particular, in order to avoid coupled-bunch instability, we consider that cooling water temperature for the cavity should be changed to shift frequencies of higher order modes (HOM) to avoid beam revolution lines. To obtain the relation between the temperature dependence of amount of frequency shift in each HOM and cavity body temperature, we carried out the measurement by changing cavity body temperature. From the measurement data, we calculate the required temperature variation. We summarize the results and describe the system design.

  2. A proposed NSLS x-ray ring upgrade using B factory technology

    SciTech Connect

    Blum, E.B.

    1995-05-01

    A proposed upgrade to the NSLS X-Ray Ring is described that will allow the storage of a 2.4 A. 3 GeV electron beam using technology developed for the PEP-II B factory at SLAC. In this configuration, a peak flux of greater than 10{sup 16} photons/sec/0.1% bandwidth/5 mrad will be produced. The four existing 53 MHz RF cavities will be replaced with eight 476 MHz cavities. Two 952 MHz cavities will also be used to lengthen the bunch, increasing the Touschek life-time. A copper vacuum chamber will be needed to absorb the increased synchrotron radiation and a feedback system may be needed to prevent multi-bunch instabilities.

  3. Automatic local beam steering systems for NSLS x-ray storage ring: Design and implementation

    SciTech Connect

    Singh, O.V.; Nawrocky, R.; Flannigan, J.

    1991-01-01

    Recently, two local automatic steering systems, controlled by microprocessors, have been installed and commissioned in the NSLS X- Ray storage ring. In each system, the position of the electron beam is stabilized at two locations by four independent servo systems. This paper describes three aspects of the local feedback program: design; commissioning; and limitation. The system design is explained by identifying major elements such as beam position detectors, signal processors, compensation amplifiers, ratio amplifiers, trim equalizers and microprocessor feedback controllers. System commissioning involves steps such as matching trim compensation, determination of local orbit bumps, measurement of open loop responses and design of servo circuits. Several limitations of performance are also discussed. 7 refs., 2 figs.

  4. Achieving Stability Requirements for Nanoprobe and Long Beam Lines at NSLS II. A Comprehensive Study

    SciTech Connect

    Simos,N.; Fallier, M.; Hill, J.; Berman, L.; Evans-Lutterodt, K.; Broadbent, A.

    2008-06-23

    Driven by beam stability requirements at the NSLS II synchrotron, such that the desired small beam sizes and high brightness are both realized and stable, a comprehensive study has been launched seeking to provide assurances that stability at the nanometer level at critical x-ray beam-lines, is achievable, given the natural and cultural vibration environment at the selected site. The study consists of (a) an extensive investigation of the site to evaluate the existing ground vibration, in terms of amplitude, frequency content and coherence, and (b) of a numerical study of wave propagation and interaction with the infrastructure of the sensitive lines. The paper presents results from both aspects of the study.

  5. Beam measurements using visible synchrotron light at NSLS2 storage ring

    SciTech Connect

    Cheng, Weixing Bacha, Bel; Singh, Om

    2016-07-27

    Visible Synchrotron Light Monitor (SLM) diagnostic beamline has been designed and constructed at NSLS2 storage ring, to characterize the electron beam profile at various machine conditions. Due to the excellent alignment, SLM beamline was able to see the first visible light when beam was circulating the ring for the first turn. The beamline has been commissioned for the past year. Besides a normal CCD camera to monitor the beam profile, streak camera and gated camera are used to measure the longitudinal and transverse profile to understand the beam dynamics. Measurement results from these cameras will be presented in this paper. A time correlated single photon counting system (TCSPC) has also been setup to measure the single bunch purity.

  6. Preliminary Safety Analysis Report (PSAR), The NSLS 200 MeV Linear Electron Accelerator

    SciTech Connect

    Blumberg, L.N.; Ackerman, A.I.; Dickinson, T.; Heese, R.N.; Larson, R.A.; Neuls, C.W.; Pjerov, S.; Sheehan, J.F.

    1993-06-15

    The radiological, fire and electrical hazards posed by a 200 MeV electron Linear Accelerator, which the NSLS Department will install and commission within a newly assembled structure, are addressed in this Preliminary Safety Analysis Report. Although it is clear that this accelerator is intended to be the injector for a future experimental facility, we address only the Linac in the present PSAR since neither the final design nor the operating characteristics of the experimental facility are known at the present time. The fire detection and control system to be installed in the building is judged to be completely adequate in terms of the marginal hazard presented - no combustible materials other than the usual cabling associated with such a facility have been identified. Likewise, electrical hazards associated with power supplies for the beam transport magnets and accelerator components such as the accelerator klystrons and electron gun are classified as marginal in terms of potential personnel injury, cost of equipment lost, program downtime and public impact perceptions as defined in the BNL Environmental Safety and Health Manual and the probability of occurrence is deemed to be remote. No unusual features have been identified for the power supplies or electrical distribution system, and normal and customary electrical safety standards as practiced throughout the NSLS complex and the Laboratory are specified in this report. The radiation safety hazards are similarly judged to be marginal in terms of probability of occurrence and potential injury consequences since, for the low intensity operation proposed - a factor of 25 less than the maximum Linac capability specified by the vendor - the average beam power is only 0.4 watts. The shielding specifications given in this report will give adequate protection to both the general public and nonradiation workers in areas adjacent to the building as well as radiation workers within the controlled access building.

  7. Shielding NSLS-II light source: Importance of geometry for calculating radiation levels from beam losses

    NASA Astrophysics Data System (ADS)

    Kramer, S. L.; Ghosh, V. J.; Breitfeller, M.; Wahl, W.

    2016-11-01

    Third generation high brightness light sources are designed to have low emittance and high current beams, which contribute to higher beam loss rates that will be compensated by Top-Off injection. Shielding for these higher loss rates will be critical to protect the projected higher occupancy factors for the users. Top-Off injection requires a full energy injector, which will demand greater consideration of the potential abnormal beam miss-steering and localized losses that could occur. The high energy electron injection beam produces significantly higher neutron component dose to the experimental floor than a lower energy beam injection and ramped operations. Minimizing this dose will require adequate knowledge of where the miss-steered beam can occur and sufficient EM shielding close to the loss point, in order to attenuate the energy of the particles in the EM shower below the neutron production threshold (<10 MeV), which will spread the incident energy on the bulk shield walls and thereby the dose penetrating the shield walls. Designing supplemental shielding near the loss point using the analytic shielding model is shown to be inadequate because of its lack of geometry specification for the EM shower process. To predict the dose rates outside the tunnel requires detailed description of the geometry and materials that the beam losses will encounter inside the tunnel. Modern radiation shielding Monte-Carlo codes, like FLUKA, can handle this geometric description of the radiation transport process in sufficient detail, allowing accurate predictions of the dose rates expected and the ability to show weaknesses in the design before a high radiation incident occurs. The effort required to adequately define the accelerator geometry for these codes has been greatly reduced with the implementation of the graphical interface of FLAIR to FLUKA. This made the effective shielding process for NSLS-II quite accurate and reliable. The principles used to provide supplemental

  8. ADDITIONAL QUADRUPOLES AT CENTER OF LONG STRAIGHTS IN THE NSLS-II LATTICE

    SciTech Connect

    Lin, F.; Bengtsson, J.; Guo, W.; Krinsky, S.; Li, Y.; Yang, L.

    2011-03-28

    The NSLS-II storage ring lattice is comprised of 30 DBA cells arranged in 15 superperiods. There are 15 long straight sections (9.3m) for injection, RF and insertion devices and 15 shorter straights (6.6m) for insertion devices. In the baseline lattice, the short straights have small horizontal and vertical beta functions but the long straights have large horizontal beta function optimized for injection. In this paper, we explore the possibility of installing additional quadrupoles at the center of selected long straight sections in order to provide two low-beta source locations for undulators in the same straight. The required modification to the linear lattice is discussed as well as the preservation of adequate dynamic aperture required for good injection efficiency and adequate Touschek lifetime. This paper discusses the possibility of producing two low-beta source locations for optimum brightness of undulators in the long straights of NSLS-II lattice by installing additional quadrupoles at the center. The linear optics is optimized to satisfy the requirements of lattice function and properties. Nonlinear optimization for a lattice with working point at (37.16, 17.22) is performed. Considering the magnets misalignment errors and physical apertures, we calculate the frequency maps and plot the tune footprint. The results show that the modified high-low beta function lattice can achieve a modest dynamic aperture in this preliminary study. Further work will continue to expand the dynamic aperture to meet the requirement of good injection efficiency and sufficient Touschek lifetime.

  9. Bacterial mixture analysis with Raman chemical imaging microspectroscopy

    NASA Astrophysics Data System (ADS)

    Tripathi, Ashish; Jabbour, Rabih E.; Guicheteau, Jason A.; Christesen, Steven D.; Emge, Darren K.; Jensen, Janet L.; Snyder, A. Peter

    2009-05-01

    Raman chemical imaging microspectroscopy (RCIM) is being evaluated as a technology for waterborne pathogen detection. Binary and ternary mixtures including combinations of polystyrene beads, Grampositive Bacillus anthracis and B. atrophaeus spores, B. cereus vegetative cells, and Gram-negative E. coli cells were investigated by RCIM for differentiation and characterization purposes. We have demonstrated the ability of RCIM, in combination with Pearson's cross correlation and multivariate principal components analysis data reduction techniques, to differentiate these components in the same field of view (FOV). Conventional applications of RCIM consist of differentiating relatively broad areas in a FOV. Here, RCIM is expanded in its capabilities to differentiate and distinguish between different micron size species in single particles and clusters of mixed species.

  10. Raman Microspectroscopy Analysis in the Treatment of Acanthamoeba Keratitis

    PubMed Central

    Rusciano, Giulia; Capriglione, Paola; Pesce, Giuseppe; Del Prete, Salvatore; Cennamo, Gilda; Di Cave, David; Cerulli, Luciano; Sasso, Antonio

    2013-01-01

    Acanthamoeba keratitis is a rare but serious corneal disease, often observed in contact lens wearers. Clinical treatment of infected patients frequently involves the use of polyhexamethylene biguanide (PHMB), a polymer used as a disinfectant and antiseptic, which is toxic also for the epithelial cells of the cornea. Prompt and effective diagnostic tools are hence highly desiderable for both starting early therapy and timely suspension of the treatment. In this work we use Raman microspectroscopy to analyse in vitro a single Acanthamoeba cell in cystic phase. In particular, we investigate the effect of PHMB at the single-cell level, providing useful information on both the underlying biochemical mechanism and the time frame for Acanthamoeba eradication in ocular infections. Furthermore, we demonstrate that Raman spectroscopy, in conjunction with standard multivariate analysis methods, allows discriminating between live and dead Acanthamoebas, which is fundamental to optimizing patients’ treatment. PMID:23977228

  11. Raman microspectroscopy of nanodiamond-induced structural changes in albumin.

    PubMed

    Svetlakova, Anastasiya S; Brandt, Nikolay N; Priezzhev, Alexander V; Chikishev, Andrey Yu

    2015-04-01

    Nanodiamonds (NDs) are promising agents for theranostic applications due to reported low toxicity and high biocompatibility, which is still being extensively tested on cellular, tissue, and organism levels. It is presumed that for experimental and future clinical applications, NDs will be administered into the organism via the blood circulation system. In this regard, the interaction of NDs with blood components needs to be thoroughly studied. We studied the interaction of carboxylated NDs (cNDs) with albumin, one of the major proteins of blood plasma. After 2-h long in vitro incubation in an aqueous solution of the protein, 100-nm cNDs were dried and the dry samples were studied with the aid of Raman microspectroscopy. The spectroscopic data indicate significant conformational changes that can be due to cND–protein interaction. A possible decrease in the functional activity of albumin related to the conformational changes must be taken into account in the in vivo applications.

  12. Raman microspectroscopy of nanodiamond-induced structural changes in albumin

    NASA Astrophysics Data System (ADS)

    Svetlakova, Anastasiya S.; Brandt, Nikolay N.; Priezzhev, Alexander V.; Chikishev, Andrey Yu.

    2015-04-01

    Nanodiamonds (NDs) are promising agents for theranostic applications due to reported low toxicity and high biocompatibility, which is still being extensively tested on cellular, tissue, and organism levels. It is presumed that for experimental and future clinical applications, NDs will be administered into the organism via the blood circulation system. In this regard, the interaction of NDs with blood components needs to be thoroughly studied. We studied the interaction of carboxylated NDs (cNDs) with albumin, one of the major proteins of blood plasma. After 2-h long in vitro incubation in an aqueous solution of the protein, 100-nm cNDs were dried and the dry samples were studied with the aid of Raman microspectroscopy. The spectroscopic data indicate significant conformational changes that can be due to cND-protein interaction. A possible decrease in the functional activity of albumin related to the conformational changes must be taken into account in the in vivo applications.

  13. Applications of Synchrotron Infrared Microspectroscopy to the Study of Fingerprints

    NASA Astrophysics Data System (ADS)

    Wilkinson, Tommy J.; Perry, Dale L.; Martin, Michael C.; McKinney, Wayne R.

    2001-03-01

    Synchrotron infrared microspectroscopy has been used to study chemical markers and profiles of human fingerprints in the mid-infrared region (4000-400 cm-1). Band intensities and band intensity ratios for functional groups of chemical molecules that are inherent to the fingerprint's chemical system are discussed in the context of molecular species. These species can be identified by comparison to infrared spectra that have been reported previously for identified chemical components. Mapping of chemical heterogeneities using spectral markers is presented and discussed. Changes in the chemistry of the fingerprint will be discussed in the context of the aging process which is reflected in the changes in the infrared spectra. agraph This work was supported by the Center for Science and Engineering Education (CSEE) at Lawrence Berkeley National Laboratory, and the Director, Office of Basic Energy Sciences, Materials Science Division, of the U. S. Department of Energy under Contract No. DE-AC03-76SF00098.

  14. Application of FT IR microspectroscopy in diagnosing thyroid neoplasms

    NASA Astrophysics Data System (ADS)

    Schultz, Christian P.; Liu, Kan-Zhi; Salamon, Elizabeth A.; Riese, Karl T.; Mantsch, Henry H.

    1999-05-01

    Tissue biopsies and fine-needle aspirates (FNA) of patients with suspected benign or malignant thyroid neoplasms were investigated by infrared microspectroscopy and multivariate statistical methods. Unsupervised cluster analysis revealed four different spectral patterns for the aspirates analyzed, corresponding to colloid goiter, adenoma, carcinomas and negative diagnoses. Infrared microspectroscopic measurements of neoplastic cells on infrared transparent slides provide a potentially new tool for diagnostic screening of these FNA. Biopsy material obtained during surgical removal of gland tissue, was successfully used to generate statistically significant criteria for the distinction of neoplastic from normal tissue. Bivariate histogram plots demonstrate that two selected parameters, DNA and protein, are sufficient to separate control tissue from adenoma and carcinomas

  15. [Application of FTIR micro-spectroscopy in the tribology].

    PubMed

    Hu, Zhi-meng

    2002-10-01

    The wave number of characteristic absorption peak nu asC-O-C of the polyester formed on the frictional process were determined by Fourier Transform Infrared (FTIR) Micro-spectroscopy, and the wave number displacement of characteristic absorption peak nu asC-O-C was analyzed based on the conversion mass of polyester formed. The internal relations between anti-wear order rule of hydroxyl fatty acids and vibration absorption peak nu asC-O-C of polyester formed by hydroxyl fatty acids was deduced according to these results, and the anti-wear order of hydroxyl fatty acids was reasonably explained, that is 13, 14-di-hydroxydocosanoic acid > 13 (14)-monohydroxydocosanoic acid = 9,10-dihydroxyoctadecanoic acid > 9,10,12-trihydroxyoctadecanoic acid > 9(10)-monohydroxyoctadecanoic acid. A net polyester film is formed by 13, 14-dihydroxydocosanoic acid and a linear polyester film is formed by 9, (10)-monohydroxyoctadecanoic acid and 13(14)-monohydroxydocosanoic acid.

  16. Advances in photo-thermal infrared imaging microspectroscopy

    NASA Astrophysics Data System (ADS)

    Furstenberg, Robert; Kendziora, Chris; Papantonakis, Michael; Nguyen, Viet; McGill, Andrew

    2013-05-01

    There is a growing need for chemical imaging techniques in many fields of science and technology: forensics, materials science, pharmaceutical and chemical industries, just to name a few. While FTIR micro-spectroscopy is commonly used, its practical resolution limit of about 20 microns or more is often insufficient. Raman micro-spectroscopy provides better spatial resolution (~1 micron), but is not always practical because of samples exhibiting fluorescence or low Raman scattering efficiency. We are developing a non-contact and non-destructive technique we call photo-thermal infrared imaging spectroscopy (PT-IRIS). It involves photo-thermal heating of the sample with a tunable quantum cascade laser and measuring the resulting increase in thermal emission with an infrared detector. Photo-thermal emission spectra resemble FTIR absorbance spectra and can be acquired in both stand-off and microscopy configurations. Furthermore, PT-IRIS allows the acquisition of absorbance-like photo-thermal spectra in a reflected geometry, suitable for field applications and for in-situ study of samples on optically IR-opaque substrates (metals, fabrics, paint, glass etc.). Conventional FTIR microscopes in reflection mode measure the reflectance spectra which are different from absorbance spectra and are usually not catalogued in FTIR spectral libraries. In this paper, we continue developing this new technique. We perform a series of numerical simulations of the laser heating of samples during photo-thermal microscopy. We develop parameterized formulas to help the user pick the appropriate laser illumination power. We also examine the influence of sample geometry on spectral signatures. Finally, we measure and compare photo-thermal and reflectance spectra for two test samples.

  17. Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C

    PubMed Central

    Orville, Allen M.; Buono, Richard; Cowan, Matt; Héroux, Annie; Shea-McCarthy, Grace; Schneider, Dieter K.; Skinner, John M.; Skinner, Michael J.; Stoner-Ma, Deborah; Sweet, Robert M.

    2011-01-01

    The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population. PMID:21525643

  18. Correlated Single-Crystal Electronic Absorption Spectroscopy and X-ray Crystallography at NSLS Beamline X26-C

    SciTech Connect

    A Orville; R Buono; M Cowan; A Heroux; G Shea-McCarthy; D Schneider; J Skinner; M Skinner; D Stoner-Ma; R Sweet

    2011-12-31

    The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

  19. Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C

    SciTech Connect

    Orville, A.M.; Buono, R.; Cowan, M.; Heroux, A.; Shea-McCarthy, G.; Schneider, D. K.; Skinner, J. M.; Skinner, M. J.; Stoner-Ma, D.; Sweet, R. M.

    2011-05-01

    The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

  20. Comparative Study of Vibration Stability at Operating Light Source Facilities and Lessons Learned in Achieving NSLS II Stability Goals

    SciTech Connect

    Simos,N.; Fallier, M.; Amick, H.

    2008-06-23

    In an effort to ensure that the stability goals of the NSLS II will be met once the accelerator structure is set on the selected BNL site a comprehensive evaluation of the ground vibration observed at existing light source facilities has been undertaken. The study has relied on measurement data collected and reported by the operating facilities as well as on new data collected in the course of this study. The primary goal of this comprehensive effort is to compare the green-field conditions that exist in the various sites both in terms of amplitude as well as frequency content and quantify the effect of the interaction of these accelerator facilities with the green-field vibration. The latter represents the ultimate goal of this effort where the anticipated motion of the NSLS II ring is estimated prior to its construction and compared with the required stability criteria.

  1. Optimisation of NSLS-II Blade X-ray Beam Position Monitors: from Photoemission type to Diamond Detector

    SciTech Connect

    ILINSKI P.

    2012-07-10

    Optimisation of blade type x-ray beam position monitors (XBPM) was performed for NSLS-II undulator IVU20. Blade material, con and #64257;guration and operation principle was analysed in order to improve XBPM performance. Optimisation is based on calculation of the XBPM signal spatial distribution. Along with standard photoemission type XBPM a Diamond Detector Blades (DDB) were analysed as blades for XBPMs. DDB XBPMs can help to overcome drawbacks of the photoemission blade XBPMs.

  2. The sub-micron resolution X-ray spectroscopy beamline at NSLS-II

    NASA Astrophysics Data System (ADS)

    De Andrade, V.; Thieme, J.; Northrup, P.; Yao, Y.; Lanzirotti, A.; Eng, P.; Shen, Q.

    2011-09-01

    For many research areas such as life, environmental, earth or material sciences, novel analytical resources have to be developed for an advance understanding of complex natural and engineered systems that are heterogeneous on the micron to the tenths of microns scale. NSLS-II at BNL will be a synchrotron radiation source with an ultra-high brilliance delivering a high current (500 mA). One of the 1st six NSLS-II beamlines will be the Sub-micron Resolution X-ray spectroscopy beamline (SRX), dedicated as an analytical tool to study complex systems on a sub-micron length scale. SRX will comprise two branches thanks to a canted setup with two undulators: the first branch using Kirkpatrick-Baez mirrors as focusing optics will cover the energy range of 4.65-23 keV, allowing for XANES experiments from the Ti to the Rh K-edge. Thanks to a horizontally deflecting double crystal monochromator with maximum stability, a set of slits located on the secondary source, and two sets of complementary and quickly interchangeable KB mirrors, spectroscopy with very high spectral and spatial resolution will be achieved. The spot size will almost fully cover a range from 60×60 to 1300×500 nm 2, providing an attractive adaptability of the observation scale. A 1.5 m long IVU21 will serve as a light source. The expected high flux in a sub-micron-spot (5×10 12 and 7×10 13 ph s -1 at maximum and lowest resolutions) will open new possibilities for spectromicroscopy of trace elements. The 2nd canted undulator will serve as an independent light source for the second branch designed for experiments with X-ray energies in the range of 2-15 keV. Using Fresnel zone plates, the spatial resolution aimed for is around 30 nm with up to 7×10 9 ph s -1 in the spot. This branch would be attractive for many biological applications from life and environmental science due to low-Z elements of interest within that energy range. In both experimental stations, X-ray fluorescence will be used for imaging

  3. Shielding NSLS-II light source: Importance of geometry for calculating radiation levels from beam losses

    SciTech Connect

    Kramer, S. L.; Ghosh, V. J.; Breitfeller, M.; Wahl, W.

    2016-08-10

    We present that third generation high brightness light sources are designed to have low emittance and high current beams, which contribute to higher beam loss rates that will be compensated by Top-Off injection. Shielding for these higher loss rates will be critical to protect the projected higher occupancy factors for the users. Top-Off injection requires a full energy injector, which will demand greater consideration of the potential abnormal beam miss-steering and localized losses that could occur. The high energy electron injection beam produces significantly higher neutron component dose to the experimental floor than a lower energy beam injection and ramped operations. Minimizing this dose will require adequate knowledge of where the miss-steered beam can occur and sufficient EM shielding close to the loss point, in order to attenuate the energy of the particles in the EM shower below the neutron production threshold (<10 MeV), which will spread the incident energy on the bulk shield walls and thereby the dose penetrating the shield walls. Designing supplemental shielding near the loss point using the analytic shielding model is shown to be inadequate because of its lack of geometry specification for the EM shower process. To predict the dose rates outside the tunnel requires detailed description of the geometry and materials that the beam losses will encounter inside the tunnel. Modern radiation shielding Monte-Carlo codes, like FLUKA, can handle this geometric description of the radiation transport process in sufficient detail, allowing accurate predictions of the dose rates expected and the ability to show weaknesses in the design before a high radiation incident occurs. The effort required to adequately define the accelerator geometry for these codes has been greatly reduced with the implementation of the graphical interface of FLAIR to FLUKA. In conclusion, this made the effective shielding process for NSLS-II quite accurate and reliable. The principles

  4. Shielding NSLS-II light source: Importance of geometry for calculating radiation levels from beam losses

    DOE PAGES

    Kramer, S. L.; Ghosh, V. J.; Breitfeller, M.; ...

    2016-08-10

    We present that third generation high brightness light sources are designed to have low emittance and high current beams, which contribute to higher beam loss rates that will be compensated by Top-Off injection. Shielding for these higher loss rates will be critical to protect the projected higher occupancy factors for the users. Top-Off injection requires a full energy injector, which will demand greater consideration of the potential abnormal beam miss-steering and localized losses that could occur. The high energy electron injection beam produces significantly higher neutron component dose to the experimental floor than a lower energy beam injection and rampedmore » operations. Minimizing this dose will require adequate knowledge of where the miss-steered beam can occur and sufficient EM shielding close to the loss point, in order to attenuate the energy of the particles in the EM shower below the neutron production threshold (<10 MeV), which will spread the incident energy on the bulk shield walls and thereby the dose penetrating the shield walls. Designing supplemental shielding near the loss point using the analytic shielding model is shown to be inadequate because of its lack of geometry specification for the EM shower process. To predict the dose rates outside the tunnel requires detailed description of the geometry and materials that the beam losses will encounter inside the tunnel. Modern radiation shielding Monte-Carlo codes, like FLUKA, can handle this geometric description of the radiation transport process in sufficient detail, allowing accurate predictions of the dose rates expected and the ability to show weaknesses in the design before a high radiation incident occurs. The effort required to adequately define the accelerator geometry for these codes has been greatly reduced with the implementation of the graphical interface of FLAIR to FLUKA. In conclusion, this made the effective shielding process for NSLS-II quite accurate and reliable. The

  5. SERVER DEVELOPMENT FOR NSLS-II PHYSICS APPLICATIONS AND PERFORMANCE ANALYSIS

    SciTech Connect

    Shen, G.; Kraimer, M.

    2011-03-28

    The beam commissioning software framework of NSLS-II project adopts a client/server based architecture to replace the more traditional monolithic high level application approach. The server software under development is available via an open source sourceforge project named epics-pvdata, which consists of modules pvData, pvAccess, pvIOC, and pvService. Examples of two services that already exist in the pvService module are itemFinder, and gather. Each service uses pvData to store in-memory transient data, pvService to transfer data over the network, and pvIOC as the service engine. The performance benchmarking for pvAccess and both gather service and item finder service are presented in this paper. The performance comparison between pvAccess and Channel Access are presented also. For an ultra low emittance synchrotron radiation light source like NSLS II, the control system requirements, especially for beam control are tight. To control and manipulate the beam effectively, a use case study has been performed to satisfy the requirement and theoretical evaluation has been performed. The analysis shows that model based control is indispensable for beam commissioning and routine operation. However, there are many challenges such as how to re-use a design model for on-line model based control, and how to combine the numerical methods for modeling of a realistic lattice with the analytical techniques for analysis of its properties. To satisfy the requirements and challenges, adequate system architecture for the software framework for beam commissioning and operation is critical. The existing traditional approaches are self-consistent, and monolithic. Some of them have adopted a concept of middle layer to separate low level hardware processing from numerical algorithm computing, physics modelling, data manipulating and plotting, and error handling. However, none of the existing approaches can satisfy the requirement. A new design has been proposed by introducing service

  6. NSLS-II HIGH LEVEL APPLICATION INFRASTRUCTURE AND CLIENT API DESIGN

    SciTech Connect

    Shen, G.; Yang; L.; Shroff; K.

    2011-03-28

    The beam commissioning software framework of NSLS-II project adopts a client/server based architecture to replace the more traditional monolithic high level application approach. It is an open structure platform, and we try to provide a narrow API set for client application. With this narrow API, existing applications developed in different language under different architecture could be ported to our platform with small modification. This paper describes system infrastructure design, client API and system integration, and latest progress. As a new 3rd generation synchrotron light source with ultra low emittance, there are new requirements and challenges to control and manipulate the beam. A use case study and a theoretical analysis have been performed to clarify requirements and challenges to the high level applications (HLA) software environment. To satisfy those requirements and challenges, adequate system architecture of the software framework is critical for beam commissioning, study and operation. The existing traditional approaches are self-consistent, and monolithic. Some of them have adopted a concept of middle layer to separate low level hardware processing from numerical algorithm computing, physics modelling, data manipulating, plotting, and error handling. However, none of the existing approaches can satisfy the requirement. A new design has been proposed by introducing service oriented architecture technology. The HLA is combination of tools for accelerator physicists and operators, which is same as traditional approach. In NSLS-II, they include monitoring applications and control routines. Scripting environment is very important for the later part of HLA and both parts are designed based on a common set of APIs. Physicists and operators are users of these APIs, while control system engineers and a few accelerator physicists are the developers of these APIs. With our Client/Server mode based approach, we leave how to retrieve information to the

  7. [Microalgae Species Identification Study with Raman Microspectroscopy Technology].

    PubMed

    Shao, Yong-ni; Pan, Jian; Jiang, Lu-lu; He, Yong

    2015-07-01

    Identification and classification of microalgae are basis and premise in the study of physiological and biochemical characteristics for microalgae. Microalgae cells mainly consist of five kinds of biological molecules, including proteins, carbonhydrates, lipids, nucleic acids and pigments. These five kinds of biological molecules contents with different ratio in microalgae cells can be utilized to identify microalgae species as a supplement method. This paper investigated the application of Raman microspectroscopy technology in the field of rapid identification on different algae species such as aschlorella sp. and chlamydomonas sp. . Cultivated in the same conditions of culture medium, illumination duration and intensity, these two kinds of species of microalgae cells were immobilized by using agar, and then the samples were placed under 514. 5 nm Raman laser to collect Raman spectra of different growth periods of different species. An approach to remove fluorescence background in Raman spectra called Rolling Circle Filter (RCF) algorithm was adopted to remove the fluorescent background, and then some preprocessing methods were used to offset the baseline and smooth method of Savitzky-Golay was tried to make the spectra curves of total 80 samples smoother. Then 50 samples were randomly extracted from 80 samples for modeling, and the remaining 30 samples for independent validation. This paper adopted different pretreatment methods, and used the partial least squares (PLS) to establish model between the spectral data and the microalgae species, then compared the effects of different pretreatment methods. The results showed that with Raman microspectroscopy technology, the pretreatment method of max-peak ratio standardization was a more effective identification approach which utilizes the different content ratios of pigments of different microalgae species. This method could efficiently eliminate the influence on Raman signal due to different growth stages of

  8. Nonlinear photothermal Mid-Infrared Microspectroscopy with Superresolution

    NASA Astrophysics Data System (ADS)

    Erramilli, Shyamsunder; Mertiri, Alket; Liu, Hui; Totachawattana, Atcha; Hong, Mi; Sander, Michelle

    2015-03-01

    We describe a nonlinear method for breaking the diffraction limit in mid-infrared microscopy using nonlinear photothermal microspectroscopy. A Quantum Cascade Laser (QCL) tuned to an infrared active vibrational molecular normal mode is used as the pump laser. A low-phase noise Erbium-doped fiber (EDFL) laser is used as the probe. When the incident intensity of the mid-infrared pump laser is increased past a critical threshold, a nanobubble is nucleated, strongly modulating the scatter of the probe beam, in agreement with prior work. Remarkably, we have also found that the photothermal spectral signature of the mid-infrared absorption bifurcates and is strongly narrowed, consistent with an effective ``mean-field'' theory of the observed pitchfork bifurcation. This ultrasharp narrowing can be exploited to obtain mid-infrared images with a resolution that breaks the diffraction limit, without the need of mechanical scanning near-field probes. The method provides a powerful new tool for hyperspectral label-free mid-infrared imaging and characterization of biological tissues and materials science and engineering. We thank our collaborators H. Altug, L. D. Ziegler, J. Mertz, for their advice and generous loan of equipment.

  9. Biological infrared microspectroscopy at the National Synchrotron Light Source

    NASA Astrophysics Data System (ADS)

    Miller, Lisa M.; Carr, G. Lawrence; Williams, Gwyn P.; Sullivan, Michael; Chance, Mark R.

    2000-06-01

    Beamline U2B at the National Synchrotron Light Source has been designed and built as an infrared beamline dedicated to the study of biomedical problems. In 1997, the horizontal and vertical acceptances of Beamline U2B were increased in order to increase the overall flux of the beamline. A wedged, CVD diamond window separates the UHV vacuum of the VUV ring from the rough vacuum of the beamline. The endstation consists of a Nicolet Magna 860 step-scan FTIR and a NicPlan infrared microscope. The spectrometer is equipped with beamsplitter/detector combinations that permit data collection in the mid-and far-infrared regions. We have also made provisions for mounting an external detector (e.g. bolometer) for far infrared microspectroscopy. Thus far, Beamline U2B has been used to (1) perform chemical imaging of bone tissue and brain cells to address issues related to bone disease and epilepsy, respectively, and (2) examine time-resolved protein structure in the sub-millisecond folding of cytochrome c.

  10. Preparation of Soybean Seed Samples for FT-IR Microspectroscopy

    SciTech Connect

    Miller,S.; Pietrzak, L.

    2005-01-01

    Typical preparation of seed samples for infrared (IR) microspectroscopy involves imbibition of the seed for varying time periods followed by cryosectioning. Imbibition, however, may initiate germination even at 4 C with associated changes in the chemistry of the sample. We have found that it is possible to section seeds that are sufficiently hard, such as soybeans, on a standard laboratory microtome without imbibition. The use of dry sectioning of unimbibed seeds is reported here, as well as a comparison of different mounting media and modes of analysis. Glycerol, Tissue-Tek, and ethanol were used as mounting media, and the quality of the resulting spectra was assessed. Ethanol was the preferred mountant, because it dried quickly with no residue and thus did not interfere with the spectrum of interest. Analysis in transmission mode using barium fluoride windows to hold the samples was compared with transmission-reflection analysis with sections mounted on special infrared-reflecting slides. The two modes of analysis performed well in different regions of the spectrum. The mode of analysis (transmission vs. transmission-reflection) should be based on the components of greatest interest in the sample.

  11. Biological substance characterization in water matrices with Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Jabbour, Rabih E.; Tripathi, Ashish; Treado, Patrick J.; Neiss, Jason H.; Nelson, Matthew P.; Jensen, Janet L.; Snyder, A. Peter

    2007-04-01

    Raman spectroscopy has been evaluated as a candidate technology for waterborne pathogen detection. Parameters have been investigated that influence the fidelity of Raman spectra of microorganisms and protein biological substances including bacterial species and strains, susceptibility to laser induced photodamage, composition of water matrix, and organism aging in water. An important operating parameter is the laser induced photodamage threshold of a variety of biological materials. The laser induced photodamage may be minimized by operating a 532 nm continuous wave laser excitation at laser power densities below 2300 W/cm2 for Gram-positive Bacillus atrophaeus (BG) vegetative cells, 2800 W/cm2 for BG spores, and 3500 W/cm2 for Gram-negative E. coli organisms. Multivariate principal components analysis was able to discriminate six Gram-positive and Gram-negative organisms as well as five proteins between 5K and 65K mass units. B. thuringiensis, B. cereus, BG spore and vegetative preparations, and E. coli showed minimal aging effects when suspended in distilled and tap water. In general, Raman microspectroscopy of biological substances exhibited minimal spectral variability due to the age of a resting suspension, water matrix, and bacterial strain. The observed signature variability did not prevent the differentiation and characterization of bacterial genus and species and protein substances using Raman spectroscopy.

  12. Water matrix and age effects on microorganism Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Tripathi, Ashish; Jabbour, Rabih E.; Treado, Patrick J.; Nelson, Matthew P.; Snyder, A. Peter

    2010-04-01

    Raman microspectroscopy is used to probe the age and milieu parameters for suspensions of bacteria for their detection in water backgrounds. No studies have been reported on the fate of Raman signatures over time for biologicals stored in water matrices. A FALCON II Raman Chemical Imaging System (ChemImage, Pittsburgh, PA) and 532 nm laser excitation source acquired the Raman spectra. MATLAB principal components (PC) analysis software was employed for data reduction. Suspensions of Bacillus atrophaeus, Bacillus thuringiensis, and three strains of E. coli (EC) were prepared in distilled and recipe tap water. Aliquots at 5 min, 5 hr, and 1, 2, and 7 days at 25 C were dried on microscope slides in replicate. Adequate spectral differences were observed for all three organism species. Microscope analysis showed that freshly suspended Bacillus spores and EC vegetative cells, in both water matrices, remained as spores after seven days. Agar plate growth procedures showed that the bacteria were still viable even after seven days resting in both water matrices. All three bacterial species were separated based on PC analysis; however, the three EC strains coalesced. The water matrix parameter was inconsistent in its ability to separate the Raman spectra in PC plots of the five bacteria. Within each group, the time parameter poorly separated the bacterial resting suspensions as the aging proceeded. A Mahalanobis linkage distance analysis (dendrogram) for all three species and strains in both water matrices confirmed a random order for all five suspension times.

  13. The life science x-ray scattering beamline at NSLS-II

    SciTech Connect

    DiFabio, Jonathan; Chodankar, Shirish; Pjerov, Sal; Jakoncic, Jean; Lucas, Michael; Graziano, Vito; Yang, Lin; Krywka, Christina

    2016-07-27

    We report the current development status of the High Brightness X-ray Scattering for Life Sciences (or Life Science X-ray Scattering, LiX) beamline at the NSLS-II facility of Brookhaven National Laboratory. This instrument will operate in the x-ray energy range of 2.1-18 keV, provide variable beam sizes from 1 micron to ∼0.5 mm, and support user experiments in three scientific areas: (1) high-throughput solution scattering, in-line size exclusion chromatography and flow mixers-based time-resolved solution scattering of biological macro-molecules, (2) diffraction from single- and multi-layered lipid membranes, and (3) scattering-based scanning probe imaging of biological tissues. In order to satisfy the beam stability required for these experiments and to switch rapidly between different types of experiments, we have adopted a secondary source with refractive lenses for secondary focusing, a detector system consisting of three Pilatus detectors, and specialized experimental modules that can be quickly exchanged and each dedicated to a defined set of experiments. The construction of this beamline is on schedule for completion in September 2015. User experiments are expected to start in Spring 2016.

  14. 1500 MHZ Passive SRF Cavity for Bunch Lengthening in the NSLS-II Storage Ring

    SciTech Connect

    Yanagisawa,T.; Rose, J.; Grimm, T.; Bogle, A.

    2009-05-04

    NSLS-II is a new ultra-bright 3 GeV 3rd generation synchrotron radiation light source. The performance goals require operation with a beam current of 500mA and a bunch current of at least 0.5mA. Ion clearing gaps are required to suppress ion effects on the beam. The natural bunch length of 3mm is planned to be lengthened by means of a third harmonic cavity in order to increase the Touschek limited lifetime. After an extensive investigation of different cavity geometries, a passive, superconducting two-cell cavity has been selected for prototyping. The cavity is HOM damped with ferrite absorbers on the beam pipes. The two-cell cavity simplifies the tuner design, compared to having two independent cells. Tradeoffs between the damping of the higher order modes, thermal isolation associated with the large beam tubes, and overall cavity length are described. A copper prototype has been constructed, and measurements of fundamental and higher order modes will be compared to calculated values.

  15. The life science X-ray scattering beamline at NSLS-II

    DOE PAGES

    DiFabio, Jonathan; Yang, Lin; Chodankar, Shirish; ...

    2015-09-30

    We report the current development status of the High Brightness X-ray Scattering for Life Sciences (or Life Science X-ray Scattering, LiX) beamline at the NSLS-II facility of Brookhaven National Laboratory. This instrument will operate in the x-ray energy range of 2.1-18 keV, provide variable beam sizes from 1 micron to ~0.5 mm, and support user experiments in three scientific areas: (1) high-throughput solution scattering, in-line size exclusion chromatography and flow mixers-based time-resolved solution scattering of biological macro-molecules, (2) diffraction from single- and multi-layered lipid membranes, and (3) scattering-based scanning probe imaging of biological tissues. In order to satisfy the beammore » stability required for these experiments and to switch rapidly between different types of experiments, we have adopted a secondary source with refractive lenses for secondary focusing, a detector system consisting of three Pilatus detectors, and specialized experimental modules that can be quickly exchanged and each dedicated to a defined set of experiments. The construction of this beamline is on schedule for completion in September 2015. User experiments are expected to start in Spring 2016.« less

  16. The life science X-ray scattering beamline at NSLS-II

    SciTech Connect

    DiFabio, Jonathan; Yang, Lin; Chodankar, Shirish; Pjerov, Sal; Jakoncic, Jean; Lucas, Michael; Krywka, Christina; Graziano, Vito

    2015-09-30

    We report the current development status of the High Brightness X-ray Scattering for Life Sciences (or Life Science X-ray Scattering, LiX) beamline at the NSLS-II facility of Brookhaven National Laboratory. This instrument will operate in the x-ray energy range of 2.1-18 keV, provide variable beam sizes from 1 micron to ~0.5 mm, and support user experiments in three scientific areas: (1) high-throughput solution scattering, in-line size exclusion chromatography and flow mixers-based time-resolved solution scattering of biological macro-molecules, (2) diffraction from single- and multi-layered lipid membranes, and (3) scattering-based scanning probe imaging of biological tissues. In order to satisfy the beam stability required for these experiments and to switch rapidly between different types of experiments, we have adopted a secondary source with refractive lenses for secondary focusing, a detector system consisting of three Pilatus detectors, and specialized experimental modules that can be quickly exchanged and each dedicated to a defined set of experiments. The construction of this beamline is on schedule for completion in September 2015. User experiments are expected to start in Spring 2016.

  17. Specification and R and D Program on Magnet Alignment Tolerances for NSLS-II

    SciTech Connect

    Kramer,S.L.; Jain, A. K.

    2009-05-04

    The NSLS-II light source is a proposed 3 GeV storage ring, with the potential for ultra-low emittance. Despite the reduced emittance goal for the bare lattice, the closed orbit amplification factors are on average >55 in both planes, for random quadrupole alignment errors. The high chromaticity will also require strong sextupoles and the low 3 GeV energy will require large dynamic and momentum aperture to insure adequate lifetime. This will require tight alignment tolerances ({approx} 30{micro}m) on the multipole magnets during installation. By specifying tight alignment tolerances of the magnets on the support girders, the random alignment tolerances of the girders in the tunnel can be significantly relaxed. Using beam based alignment to find the golden orbit through the quadrupole centers, the closed orbit offsets in the multipole magnets will then be reduced to essentially the alignment errors of the magnets, restoring much of the dynamic aperture and lifetime of the bare lattice. Our R&D program to achieve these tight alignment tolerances of the magnets on the girders using a vibrating wire technique, will be discussed and initial results presented.

  18. Spatially resolving variations in giant magnetoresistance, undetectable with four-point probe measurements, using infrared microspectroscopy

    SciTech Connect

    Kelley, C. S.; Thompson, S. M.; Illman, M. D.; LeFrancois, S.; Dumas, P.

    2012-10-15

    Magnetorefractive infrared (IR) microspectroscopy is demonstrated to resolve spatial variations in giant magnetoresistance (GMR) and, by modelling, provide an insight into the origin of the variations. Spatial variations are shown to be masked in conventional four-point probe electrical or IR spectral measurements. IR microspectroscopy was performed at the SMIS beamline at the SOLEIL synchrotron, modified to enable measurements in magnetic fields. A GMR gradient was induced in a CoFe/Cu multilayer sample by annealing in a temperature gradient. Modelling revealed that variations in GMR at 900 Oe could be attributed to local variations in interlayer coupling locally changing the switching field.

  19. Rapid diagnosis of liver fibrosis using multimodal multiphoton nonlinear optical microspectroscopy imaging.

    PubMed

    Lee, Jang Hyuk; Kim, Jong Chul; Tae, Giyoong; Oh, Myoung-Kyu; Ko, Do-Kyeong

    2013-07-01

    A multimodal multiphoton nonlinear optical (NLO) microspectroscopy imaging system was developed using a femtosecond laser and a photonic crystal fiber. Coherent anti-Stokes Raman scattering (CARS) microspectroscopy was combined with two-photon excitation fluorescence and second-harmonic generation microscopy in one platform and the system was applied to diagnose liver fibrosis. Normal and liver fibrosis tissues were clearly distinguished with the great difference from CARS spectra as well as multimodal multiphoton NLO images. We expect the system to be a rapid diagnosis tool for liver fibrosis at tissue level with label-free imaging of significant biochemical components.

  20. Detection of pesticide effects in human keratinocytes by means of Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Perna, G.; Lasalvia, M.; Castro, A.; Mezzenga, E.; L'Abbate, N.; Biagi, P. F.; Capozzi, V.

    2009-08-01

    Biochemical modifications of single cells of human keratinocytes exposed to different concentrations of chlorpyriphos solutions were detected by means of Raman microspectroscopy. The modifications mainly consist of breakdown of amide linkage between aminoacids. Fragmentation of DNA bases and single aminoacids occurs as well. The protein and DNA damage are already detectable at a chlorpyriphos concentration value (10-6M), which is at least three orders of magnitude lower than the concentration estimated as cytotoxic (10-3M). Raman microspectroscopy technique results to be a very sensitive technique to detect molecular changes even in single human cells exposed to toxic pesticide.

  1. Comparison of hair from rectum cancer patients and from healthy persons by Raman microspectroscopy and imaging

    NASA Astrophysics Data System (ADS)

    Wei, Xiaoli; Wang, Xin; Fang, Yusheng; Huang, Qing

    2013-09-01

    In this work, Raman microspectroscopy and imaging was employed to analyze cancer patients' hair tissue. The comparison between the hair from rectum cancer patients and the hair from healthy people reveals some remarkable differences, such as for the rectum cancer patients, there are more lipids but less content of α-helix proteins in the hair medulla section. Though more statistic data are required to establish universary rules for practical and accurate diagnosis, this work based on case study demonstrates the possibility of applying Raman microspectroscopy to reveal abnormality in non-cancer tissues such as hair in order to predict and diagnose cancers.

  2. Electron beam stability and beam peak to peak motion data for NSLS X-Ray storage ring

    SciTech Connect

    Singh, O.

    1993-07-01

    In the past two years, a significant reduction in electron beam motion has been achieved at the NSLS X-Ray storage ring. The implementation of global analog orbit feedbacks, based on a harmonics correction scheme, has reduced the beam motion globally. Implementation of six local analog feedback systems has reduced the beam motion even further at the corresponding beam line straight sections. This paper presents beam motion measurements, showing the improvement due to the feedback systems. Beam motion is measured using a spectrum analyzer and data is presented at various frequencies, where peaks were observed. Finally, some of the beam motion sources are discussed.

  3. Synchrotron IR microspectroscopy for protein structure analysis: Potential and questions

    DOE PAGES

    Yu, Peiqiang

    2006-01-01

    Synchrotron radiation-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced technique to the study of pure protein inherent structure at a cellular level in biological tissues. In this review, a novel approach was introduced to show the potential of the newly developed, advancedmore » synchrotron-based analytical technology, which can be used to localize relatively “pure“ protein in the plant tissues and relatively reveal protein inherent structure and protein molecular chemical make-up within intact tissue at cellular and subcellular levels. Several complex protein IR spectra data analytical techniques (Gaussian and Lorentzian multi-component peak modeling, univariate and multivariate analysis, principal component analysis (PCA), and hierarchical cluster analysis (CLA) are employed to relatively reveal features of protein inherent structure and distinguish protein inherent structure differences between varieties/species and treatments in plant tissues. By using a multi-peak modeling procedure, RELATIVE estimates (but not EXACT determinations) for protein secondary structure analysis can be made for comparison purpose. The issues of pro- and anti-multi-peaking modeling/fitting procedure for relative estimation of protein structure were discussed. By using the PCA and CLA analyses, the plant molecular structure can be qualitatively separate one group from another, statistically, even though the spectral assignments are not known. The synchrotron-based technology provides a new approach for protein structure research in

  4. Analysis of Wilhelm Ostwald's "Colour Organ" with Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Bridarolli, Alexandra; Atak, Sefkan; Herm, Christoph

    2016-11-01

    The "Scientific Colour Organ" is a collection of 680 pigment powders, created by the chemist Wilhelm Ostwald in 1925 as a means to represent his colour system. Today, it remains a leading part of colour theory. Analysis of these materials was undertaken to understand how the colour system was realised and to gain indications for preservation of the collection to which it belongs. Dispersive Raman microspectroscopy was applied directly to the powders, as well as using alternative techniques to suppress fluorescence. Barium sulphate was detected in all of the samples with one exception. Portable X-ray fluorescence revealed that this compound was a constituent of lithopone pigment. Raman spectroscopy furthermore revealed synthetic ultramarine (C.I. PB 29) as well as six different synthetic organic pigments and dyes (C.I. PY3; C.I. PO5; C.I. PR81:1; C.I. PV2 and two different triarylmethane dyes). Thin-layer chromatography was applied to determine the exact combination of dyes causing the gradual change in colour of each powder compared to the adjacent samples. With the exception of triarylmethane, the synthetic organic dyes could be identified with Raman spectroscopy directly on the chromatographic plate. The efficiency of thin-layer chromatography combined with Raman spectroscopy for identification of organic pigments could thus be shown. X-ray fluorescence indicated the presence of tungsten-molybdenum lakes in some samples. Comparison of the analytical results to information published by Oswald in 1917 showed that he switched to more light-stable synthetic organic pigments used for his "Scientific Colour Organ".

  5. The scanning transmission x-ray microscope at the NSLS: From XANES to cryo

    SciTech Connect

    Maser, J.; Chapman, H.; Jacobsen, C.

    1995-12-31

    The Stony Brook scanning transmission x-ray microscope (STXM) has been operated at the XIA beamline at the NSLS since 1989. A large number of users have used it to study biological and material science samples. The authors report on changes that have been performed in the past year, and present recent results. To stabilize the position of the micro probe when doing spectral scans at high spatial resolution, they have constructed a piezo-driven flexure stage which carries out the focusing motion of the zone plate needed when changing the wavelength. To overcome the detector limitation set by saturation of the gas-flow counter at count rates around 1 MHz, they are installing an avalanche photo diode with an active quenching circuit which they expect to respond linearly to count rates in excess of 10 MHz. They have improved the enclosure for STXM to improve the stability of the Helium atmosphere while taking data. This reduces fluctuations of beam absorption and, therefore, noise in the image. A fast shutter has been installed in the beam line. The authors are also developing a cryo-STXM which is designed for imaging frozen hydrated samples at temperatures below 120 K. At low temperatures, radiation sensitive samples can tolerate a considerably higher radiation dose than at room temperature. This should improve the resolution obtainable from biological samples and should make recording of multiple images of the same sample area possible while minimizing the effects of radiation damage. This should enable them to perform elemental and chemical mapping at high resolution, and to record the large number of views needed for 3D reconstruction of the object.

  6. Three Biomedical Beamlines at NSLS-II for Macromolecular Crystallography and Small-Angle Scattering

    NASA Astrophysics Data System (ADS)

    Schneider, D. K.; Berman, L. E.; Chubar, O.; Hendrickson, W. A.; Hulbert, S. L.; Lucas, M.; Sweet, R. M.; Yang, L.

    2013-03-01

    We report on the status of the development of three beamlines for the National Synchrotron Light Source-II (NSLS-II), two for macromolecular crystallography (MX), and one for wide- and small-angle x-ray scattering (SAXS). Funded by the National Institutes of Health, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX) is scheduled to begin operation by 2015. The two MX beamlines share a sector with identical canted in-vacuum undulators (IVU21). The microfocusing FMX beamline on the inboard branch employs a two-stage horizontal source demagnification scheme, will cover an energy range of 5 - 23 keV, and at 12.7 keV will focus a flux of up to 1013 ph/s into a spot of 1 μm width. The companion AMX beamline on the short outboard branch of the sector is tunable in the range of 5 - 18 keV and has a native focus of 4 μm (h) × 2 μm (v). This robust beamline will be highly automated, have high throughput capabilities, and with larger beams and low divergence will be well suited for structure determinations on large complexes. The high brightness SAXS beamline, LIX, will provide multiple dynamic and static experimental systems to support scientific programs in solution scattering, membrane structure determination, and tissue imaging. It will occupy a different sector, equipped with a single in-vacuum undulator (IVU23). It can produce beams as small as 1 μm across, and with a broad energy range of 2.1 - 18 keV it will support anomalous SAXS.

  7. Distinction of broken cellular wall Ganoderma lucidum spores and G. lucidum spores using FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Xianliang; Liu, Xingcun; Sheng, Daping; Huang, Dake; Li, Weizu; Wang, Xin

    2012-11-01

    In this paper, FTIR microspectroscopy was used to identify broken cellular wall Ganoderma lucidum spores and G. lucidum spores. For IR spectra, broken cellular wall G. lucidum spores and G. lucidum spores were mainly different in the regions of 3000-2800, 1660-1600, 1400-1200 and 1100-1000 cm-1. For curve fitting, the results showed the differences in the protein secondary structures and the polysaccharide structures/content between broken cellular wall G. lucidum spores and G. lucidum spores. Moreover, the value of A1078/A1741 might be a potentially useful factor to distinguish broken cellular wall G. lucidum spores from G. lucidum spores. Additionally, FTIR microspectroscopy could identify broken cellular wall G. lucidum spores and G. lucidum spores accurately when it was combined with hierarchical cluster analysis. The result suggests FTIR microspectroscopy is very simple and efficient for distinction of broken cellular wall G. lucidum spores and G. lucidum spores. The result also indicates FTIR microspectroscopy may be useful for TCM identification.

  8. Unprecedented staining of polar lipids by a luminescent rhenium complex revealed by FTIR microspectroscopy in adipocytes.

    PubMed

    Bader, C A; Carter, E A; Safitri, A; Simpson, P V; Wright, P; Stagni, S; Massi, M; Lay, P A; Brooks, D A; Plush, S E

    2016-06-21

    Fourier transform infrared (FTIR) microspectroscopy and confocal imaging have been used to demonstrate that the neutral rhenium(i) tricarbonyl 1,10-phenanthroline complex bound to 4-cyanophenyltetrazolate as the ancillary ligand is able to localise in regions with high concentrations of polar lipids such as phosphatidylethanolamine (PE), sphingomyelin, sphingosphine and lysophosphatidic acid (LPA) in mammalian adipocytes.

  9. Rapid detection and quantification of milk adulteration using infrared microspectroscopy and chemometrics analysis.

    PubMed

    Santos, P M; Pereira-Filho, E R; Rodriguez-Saona, L E

    2013-05-01

    The application of attenuated total reflectance mid-infrared microspectroscopy (MIR-microspectroscopy) was evaluated as a rapid method for detection and quantification of milk adulteration. Milk samples were purchased from local grocery stores (Columbus, OH, USA) and spiked at different concentrations of whey, hydrogen peroxide, synthetic urine, urea and synthetic milk. Samples were place on a 192-well microarray slide, air-dried and spectra were collected by using MIR-microspectroscopy. Pattern recognition analysis by Soft Independent Modeling of Class Analogy (SIMCA) showed tight and well-separated clusters allowing discrimination of control samples from adulterated milk. Partial Least Squares Regression (PLSR) showed standard error of prediction (SEP) ~2.33, 0.06, 0.41, 0.30 and 0.014 g/L for estimation of levels of adulteration with whey, synthetic milk, synthetic urine, urea and hydrogen peroxide, respectively. Results showed that MIR-microspectroscopy can provide an alternative methodology to the dairy industry for screening potential fraudulent practice for economic adulteration of cow's milk. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. An instrumental approach to combining confocal microspectroscopy and 3D scanning probe nanotomography.

    PubMed

    Mochalov, Konstantin E; Chistyakov, Anton A; Solovyeva, Daria O; Mezin, Alexey V; Oleinikov, Vladimir A; Vaskan, Ivan S; Molinari, Michael; Agapov, Igor I; Nabiev, Igor; Efimov, Anton E

    2017-06-21

    In the past decade correlative microscopy, which combines the potentials of different types of high-resolution microscopies with a variety of optical microspectroscopy techniques, has been attracting increasing attention in material science and biological research. One of outstanding solutions in this area is the combination of scanning probe microscopy (SPM), which provides data on not only the topography, but also the spatial distribution of a wide range of physical properties (elasticity, conductivity, etc.), with ultramicrotomy, allowing 3D multiparametric examination of materials. The combination of SPM and ultramicrotomy (scanning probe nanotomography) is very appropriate for characterization of soft multicompound nanostructurized materials, such as polymer matrices and microstructures doped with different types of nanoparticles (magnetic nanoparticles, quantum dots, nanotubes, etc.), and biological materials. A serious problem of this technique is a lack of chemical and optical characterization tools, which may be solved by using optical microspectroscopy. Here, we report the development of an instrumental approach to combining confocal microspectroscopy and 3D scanning probe nanotomography in a single apparatus. This approach retains all the advantages of SPM and upright optical microspectroscopy and allows 3D multiparametric characterization using both techniques. As the first test of the system developed, we have performed correlative characterization of the morphology and the magnetic and fluorescent properties of fluorescent magnetic microspheres doped with a fluorescent dye and magnetic nanoparticles. The results of this study can be used to obtain 3D volume images of a specimen for most high-resolution near-field scanning probe microscopies: SNOM, TERS, AFM-IR, etc. This approach will result in development of unique techniques combining the advantages of SPM (nanoscale morphology and a wide range of physical parameters) and high-resolution optical

  11. Lighting the way to the future: An anthology of improvements, developments, and research by NSLS staff and collaborators

    SciTech Connect

    1996-10-01

    Following the commissioning phase of a scientific facility, it is essential to invent, adapt and improve new technologies so that the specification and performance of the facility is upgraded over it`s lifetime. It is equally important that staff keep their expertise and research interests at the cutting edge and contribute, based on their unique experience, to the present and next generation of experiments at existing facilities and to the specification and R and D on which the next generation of facilities will be based. A synchrotron radiation facility such as the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory supports a very wide range of science which is dependent on the breadth of the electromagnetic spectrum which is generated. Scientists from many disciplines use radiation from the far infra-red ({lambda} = 12 mm, Energy = 0.1 meV) through to extreme gamma rays ({lambda} = 4 fm, Energy = 300 MeV). All aspects of the facility need continual improvement, development and research including the source itself, the optics of beamlines, experimental concepts and the performance of detectors. This collection of papers shows the scope of past work by NSLS staff and their collaborators, serves as a reminder of their achievements and as an indicator of the range, quality and quantity of work which is required to maintain a scientific user facility at the cutting edge.

  12. Single-Crystal Raman Spectroscopy and X-ray Crystallography at Beamline X26-C of the NSLS

    SciTech Connect

    D Stoner-Ma; J Skinner; D Schneider; M Cowan; R Sweet; A Orville

    2011-12-31

    Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of 'mystery density', i.e. ambiguous or unknown features within the electron density maps, especially at {approx}2 {angstrom} resolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data.

  13. A Fast, Versatile Nanoprobe for Complex Materials: The Sub-micron Resolution X-ray Spectroscopy Beamline at NSLS-II (491st Brookhaven Lecture)

    SciTech Connect

    Thieme, Juergen

    2014-02-06

    Time is money and for scientists who need to collect data at research facilities like Brookhaven Lab’s National Synchrotron Light Source (NSLS), “beamtime” can be a precious commodity. While scanning a complex material with a specific technique and standard equipment today would take days to complete, researchers preparing to use brighter x-rays and the new sub-micron-resolution x-ray spectroscopy (SRX) beamline at the National Synchrotron Light Source II (NSLS-II) could scan the same sample in greater detail with just a few hours of beamtime. Talk about savings and new opportunities for researchers! Users will rely on these tools for locating trace elements in contaminated soils, developing processes for nanoparticles to deliver medical treatments, and much more. Dr. Thieme explains benefits for next-generation research with spectroscopy and more intense x-rays at NSLS-II. He discusses the instrumentation, features, and uses for the new SRX beamline, highlighting its speed, adjustability, and versatility for probing samples ranging in size from millimeters down to the nanoscale. He will talk about complementary beamlines being developed for additional capabilities at NSLS-II as well.

  14. Getting More From Less: Correlated Single-Crystal Spectroscopy and X-ray Crystallography at the NSLS (456th Brookhaven Lecture)

    SciTech Connect

    Orville, Allen

    2010-04-21

    By integrating different techniques to collect complementary data at beam line X26C of the National Syncrotron Light Source (NSLS), Allen Orville and his colleagues of the Macromolecular Crystallography Research Resource are providing new insights into the structures of macromolecules. During the 456th Brookhaven Lecture, on Wednesday, April 21st, Orville will describe his approach and his findings in a talk entitled “Getting More From Less: Correlated Singe-Crystal Spectroscopy and X-Ray Crystallography at the NSLS,” beginning at 4 p.m. in Berkner Hall. Refreshments will be offered before and after the lecture. During his talk, Orville will discuss his field of protein crystallography, reviewing its landmark discoveries and explaining new ways of using the NSLS and, in the future, the NSLS-II, to build on those discoveries. Allen Orville took his Ph.D. in biology from the University of Minnesota in 1997. After completing a postdoc with the Howard Hughes Medical Institute at the University of Oregon, 1997-2000, he began an assistant professor at the Georgia Institute of Technology. Orville joined BNL's Biology Department in 2006 as an associate biophysicist and was promoted to biophysicist in 2008.

  15. Raman microspectroscopy: shining a new light on reproductive medicine.

    PubMed

    Mallidis, Con; Sanchez, Victoria; Wistuba, Joachim; Wuebbeling, Frank; Burger, Martin; Fallnich, Carsten; Schlatt, Stefan

    2014-01-01

    in investigative and therapeutic reproductive medicine. However, without stringent assessment and the clear representation of the methods' findings, their true meaning cannot be revealed nor should any conclusions be hastily derived. For the potential of Raman microspectroscopy to be truly realized, the dependability and reliability of the technique and its results can only be ascertained by multidisciplinary collaborations that undertake carefully conducted, controlled and analysed studies.

  16. FT-IR Microspectroscopy of Rat Ear Cartilage

    PubMed Central

    Vidal, Benedicto de Campos; Mello, Maria Luiza S.

    2016-01-01

    Rat ear cartilage was studied using Fourier transform-infrared (FT-IR) microspectroscopy to expand the current knowledge which has been established for relatively more complex cartilage types. Comparison of the FT-IR spectra of the ear cartilage extracellular matrix (ECM) with published data on articular cartilage, collagen II and 4-chondroitin-sulfate standards, as well as of collagen type I-containing dermal collagen bundles (CBs) with collagen type II, was performed. Ear cartilage ECM glycosaminoglycans (GAGs) were revealed histochemically and as a reduction in ECM FT-IR spectral band heights (1140–820 cm-1) after testicular hyaluronidase digestion. Although ear cartilage is less complex than articular cartilage, it contains ECM components with a macromolecular orientation as revealed using polarization microscopy. Collagen type II and GAGs, which play a structural role in the stereo-arrangement of the ear cartilage, contribute to its FT-IR spectrum. Similar to articular cartilage, ear cartilage showed that proteoglycans add a contribution to the collagen amide I spectral region, a finding that does not recommend this region for collagen type II quantification purposes. In contrast to articular cartilage, the symmetric stretching vibration of –SO3- groups at 1064 cm-1 appeared under-represented in the FT-IR spectral profile of ear cartilage. Because the band corresponding to the asymmetric stretching vibration of –SO3- groups (1236–1225 cm-1) overlapped with that of amide III bands, it is not recommended for evaluation of the –SO3- contribution to the FT-IR spectrum of the ear cartilage ECM. Instead, a peak (or shoulder) at 1027–1016 cm-1 could be better considered for this intent. Amide I/amide II ratios as calculated here and data from the literature suggest that protein complexes of the ear cartilage ECM are arranged with a lower helical conformation compared to pure collagen II. The present results could motivate further studies on this tissue

  17. FT-IR Microspectroscopy of Rat Ear Cartilage.

    PubMed

    Vidal, Benedicto de Campos; Mello, Maria Luiza S

    2016-01-01

    Rat ear cartilage was studied using Fourier transform-infrared (FT-IR) microspectroscopy to expand the current knowledge which has been established for relatively more complex cartilage types. Comparison of the FT-IR spectra of the ear cartilage extracellular matrix (ECM) with published data on articular cartilage, collagen II and 4-chondroitin-sulfate standards, as well as of collagen type I-containing dermal collagen bundles (CBs) with collagen type II, was performed. Ear cartilage ECM glycosaminoglycans (GAGs) were revealed histochemically and as a reduction in ECM FT-IR spectral band heights (1140-820 cm-1) after testicular hyaluronidase digestion. Although ear cartilage is less complex than articular cartilage, it contains ECM components with a macromolecular orientation as revealed using polarization microscopy. Collagen type II and GAGs, which play a structural role in the stereo-arrangement of the ear cartilage, contribute to its FT-IR spectrum. Similar to articular cartilage, ear cartilage showed that proteoglycans add a contribution to the collagen amide I spectral region, a finding that does not recommend this region for collagen type II quantification purposes. In contrast to articular cartilage, the symmetric stretching vibration of -SO3- groups at 1064 cm-1 appeared under-represented in the FT-IR spectral profile of ear cartilage. Because the band corresponding to the asymmetric stretching vibration of -SO3- groups (1236-1225 cm-1) overlapped with that of amide III bands, it is not recommended for evaluation of the -SO3- contribution to the FT-IR spectrum of the ear cartilage ECM. Instead, a peak (or shoulder) at 1027-1016 cm-1 could be better considered for this intent. Amide I/amide II ratios as calculated here and data from the literature suggest that protein complexes of the ear cartilage ECM are arranged with a lower helical conformation compared to pure collagen II. The present results could motivate further studies on this tissue under

  18. Quantifying Carbonate and Serpentine Abundances through VSWIR Microspectroscopy

    NASA Astrophysics Data System (ADS)

    Leask, E.; Ehlmann, B. L.

    2015-12-01

    Visible and shortwave-infrared (VSWIR) reflectance spectroscopy has been used for large-scale mineral mapping on Earth and on Mars. A prototype instrument (UCIS—Ultra Compact Imaging Spectrometer), operating in microscopic mode, applies the same principles over an area the size of a traditional thin section (15-50 cm2), acquiring data over the 0.5-2.5 μm range at a spatial scale of 80 μm/pixel. This technique requires little to no sample preparation and is non-destructive, preserving rock texture. It can be used on future rovers/landers for in-situ petrology and in the lab to link spectral data acquired at large scale with rock mineralogy. We compare microscale mineral maps and abundance results from linear spectral unmixing to other techniques, including XRD, acid dissolution, and EDS/WDS mapping. Samples from the Semail Ophiolite (Oman) are used as an analogue for Martian carbonate and serpentine deposits to assess the capabilities of IR spectroscopy to discriminate carbonate from minerals with absorptions at similar wavelength positions, to determine carbonate composition and the composition of intermixed phases, and to determine their relative abundances. We find that UCIS infrared images can differentiate between carbonate phases not distinguished in XRD results. For example, in a magnesite vein sample, the bulk magnesite is spectrally distinct from another carbonate phase present only in cavities within the sample. Microprobe and EDS analyses of the sample confirm that calcite is present only as a coating within secondary porosity. Similar to SEM-EDS mapping at smaller scales, UCIS can identify rare phases contained within a few pixels (100s μm). For example, aluminum-bearing phyllosilicates in discrete clasts were found among more typical serpentine in a carbonate-cemented breccia. Signals from such rare phases are typically not detectable in XRD but are in spatially resolved microscale IR data. Collectively, data indicate that VSWIR microspectroscopy

  19. Label-free detection of tumor markers in a colon carcinoma tumor progression model by confocal Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Scalfi-Happ, Claudia; Rück, Angelika; Udart, Martin; Hauser, Carmen; Dürr, Christine; Kriebel, Martin

    2013-06-01

    Living colon carcinoma cells were investigated by confocal Raman microspectroscopy. An in vitro model of tumor progression was established. Evaluation of data sets by cluster analysis reveals that lipid bodies might be a valuable diagnostic parameter for early carcinogenesis.

  20. REQUIREMENTS AND GUIDELINES FOR NSLS EXPERIMENTAL BEAM LINE VACUUM SYSTEMS-REVISION B.

    SciTech Connect

    FOERSTER,C.

    1999-05-01

    Typical beam lines are comprised of an assembly of vacuum valves and shutters referred to as a ''front end'', optical elements to monochromatize, focus and split the photon beam, and an experimental area where a target sample is placed into the photon beam and data from the interaction is detected and recorded. Windows are used to separate sections of beam lines that are not compatible with storage ring ultra high vacuum. Some experimental beam lines share a common vacuum with storage rings. Sections of beam lines are only allowed to vent up to atmospheric pressure using pure nitrogen gas after a vacuum barrier is established to protect ring vacuum. The front end may only be bled up when there is no current in the machine. This is especially true on the VUV storage ring where for most experiments, windows are not used. For the shorter wavelength, more energetic photons of the x-ray ring, beryllium windows are used at various beam line locations so that the monochromator, mirror box or sample chamber may be used in a helium atmosphere or rough vacuum. The window separates ring vacuum from the environment of the downstream beam line components. The stored beam lifetime in the storage rings and the maintenance of desirable reflection properties of optical surfaces depend upon hydrocarbon-free, ultra-high vacuum systems. Storage ring vacuum systems will operate at pressures of {approximately} 1 x 10{sup {minus}10} Torr without beam and {approximately} 1 x 10{sup {minus}9} Torr with beam. Systems are free of hydrocarbons in the sense that no pumps, valves, etc. containing organics are used. Components are all-metal, chemically cleaned and bakeable. To the extent that beam lines share a common vacuum with the storage ring, the same criteria will hold for beam line components. The design philosophy for NSLS beam lines is to use all-metal, hydrocarbon-free front end components and recommend that experimenters use this approach for common vacuum hardware downstream of front

  1. Fluorescence microspectroscopy as a tool to study mechanism of nanoparticles delivery into living cancer cells.

    PubMed

    Arsov, Zoran; Urbančič, Iztok; Garvas, Maja; Biglino, Daniele; Ljubetič, Ajasja; Koklič, Tilen; Strancar, Janez

    2011-08-01

    Lack of better understanding of nanoparticles targeted delivery into cancer cells calls for advanced optical microscopy methodologies. Here we present a development of fluorescence microspectroscopy (spectral imaging) based on a white light spinning disk confocal microscope with emission wavelength selection by a liquid crystal tunable filter. Spectral contrasting of images was used to localize polymer nanoparticles and cell membranes labeled with fluorophores that have substantially overlapping spectra. In addition, fluorescence microspectroscopy enabled spatially-resolved detection of small but significant effects of local molecular environment on the properties of environment-sensitive fluorescent probe. The observed spectral shift suggests that the delivery of suitably composed cancerostatic alkylphospholipid nanoparticles into living cancer cells might rely on the fusion with plasma cell membrane.

  2. Identification of hematite particles in sealed glass containers for pharmaceutical uses by Raman microspectroscopy.

    PubMed

    Caudron, E; Tfayli, A; Monnier, C; Manfait, M; Prognon, P; Pradeau, D

    2011-03-25

    Raman microspectroscopy has been shown to enable the identification of micro-particles inside sealed glass containers for pharmaceutical use without any sample preparation. Raman spectra were collected from unknown particles with a maximum size of 1mm, adsorbed on the inner surface of ampoules. The particles were clearly identified as primarily hematite with traces of magnetite by their characteristic Raman spectral bands. The presence of this deposit was attributed to the projection of iron oxides during the manufacturing process. These oxide particles were not detected by the quality control process of the glass manufacturer, showing that in-process quality controls failed to detect this problem. Particle identification by Raman microspectroscopy appears to be a selective, rapid and reliable analytical procedure for quality control and assurance in the pharmaceutical industry. Identification of the particles was also helpful for evaluating the nature of the contaminant and enables consequences for the toxicological aspects of final product quality to be managed.

  3. Raman Micro-spectroscopy Study of Healthy and Burned Biological Tissue

    NASA Astrophysics Data System (ADS)

    Zarnani, Faranak; Glosser, Robert; Idris, Ahamed

    2011-10-01

    Burn injuries are a significant medical problem, and need to be treated quickly and precisely. Burned skin needs to be removed early, within hours (less than 24 hrs) of injury, when the margins of the burn are still hard to define. Studies show that treating and excising burn wounds soon after the injury prevents the wound from becoming deeper, reduces the release of proinflammatory mediators, and reduces or prevents the systemic inflammatory reaction syndrome. Also, removing burned skin prepares the affected region for skin grafting. Raman micro-spectroscopy could be used as an objective diagnostic method that will assist burn surgeons in distinguishing unburned from burned areas. As a first step in developing a diagnostic tool, we present Raman micro-spectroscopy information from normal and burned ex vivo rat skin.

  4. Competitive evaluation of data mining algorithms for use in classification of leukocyte subtypes with Raman microspectroscopy.

    PubMed

    Maguire, A; Vega-Carrascal, I; Bryant, J; White, L; Howe, O; Lyng, F M; Meade, A D

    2015-04-07

    Raman microspectroscopy has been investigated for some time for use in label-free cell sorting devices. These approaches require coupling of the Raman spectrometer to complex data mining algorithms for identification of cellular subtypes such as the leukocyte subpopulations of lymphocytes and monocytes. In this study, three distinct multivariate classification approaches, (PCA-LDA, SVMs and Random Forests) are developed and tested on their ability to classify the cellular subtype in extracted peripheral blood mononuclear cells (T-cell lymphocytes from myeloid cells), and are evaluated in terms of their respective classification performance. A strategy for optimisation of each of the classification algorithm is presented with emphasis on reduction of model complexity in each of the algorithms. The relative classification performance and performance characteristics are highlighted, overall suggesting the radial basis function SVM as a robust option for classification of leukocytes with Raman microspectroscopy.

  5. FT-IR Microspectroscopy Enhances Biological and Ecological Analysis of Algae

    SciTech Connect

    Wetzel, D.; Murdock, J

    2009-01-01

    Fourier Transform Infrared (FT-IR) microspectroscopy provides an in situ, nondestructive chemical analysis of individual algal cells. Algae play key roles in nutrient cycling and energy flow through aquatic ecosystems and are pivotal in the sequestration of inorganic nutrients (e.g., carbon, nitrogen, and phosphorus) and transformation into organic forms. However, most methods used to measure algal nutritional and physiological changes are limited to detecting whole community responses because of the relatively large quantity of material needed for analysis (i.e., milligrams to grams). The spatial resolution achievable with infrared microspectroscopy allows for the analysis of macromolecular pools (e.g., proteins, lipids, carbohydrates) in individual cells that allows species specific measurements within heterogeneous microscopic communities. Initial applications characterized molecular pools within marine macroalgae and have since progressed toward ecologically based questions concerning algal physiological responses to changing nutrient availability in marine and freshwater ecosystems.

  6. Laser trapping and assembling of nanoparticles at solution surface studied by reflection micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Wang, Shun-Fa; Yuyama, Ken-ichi; Suigiyama, Teruki; Masuhara, Hiroshi

    2015-08-01

    We present the laser power dependent behavior of optical trapping assembling of 208-nm polystyrene (PS) nanoparticles at the solution surface layer. The assembling dynamics is examined by reflection microspectroscopy as well as transmission and backscattering imaging. The transmission imaging shows that the laser irradiation at the solution surface layer forms a nanoparticle assembly, whose diameter becomes large with the increase in the laser power. The backscattering image of the assembly gives structural color, meaning that nanoparticles are periodically arranged over the whole assembly region. In reflection microspectroscopy, one band appears at long wavelength and is gradually shifted to the short wavelength with the irradiation. After the blue shift, the reflection band is located at the shorter wavelength under the laser irradiation at the higher power. We discuss these spectral changes from the viewpoint of the inter-particle distance determined by the dynamic balance between attractive optical force and repulsive electrostatic force among nanoparticles.

  7. Fourier transform infrared microspectroscopy for the analysis of the biochemical composition of C. elegans worms

    PubMed Central

    Sheng, Ming; Gorzsás, András; Tuck, Simon

    2016-01-01

    ABSTRACT Changes in intermediary metabolism have profound effects on many aspects of C. elegans biology including growth, development and behavior. However, many traditional biochemical techniques for analyzing chemical composition require relatively large amounts of starting material precluding the analysis of mutants that cannot be grown in large amounts as homozygotes. Here we describe a technique for detecting changes in the chemical compositions of C. elegans worms by Fourier transform infrared microspectroscopy. We demonstrate that the technique can be used to detect changes in the relative levels of carbohydrates, proteins and lipids in one and the same worm. We suggest that Fourier transform infrared microspectroscopy represents a useful addition to the arsenal of techniques for metabolic studies of C. elegans worms. PMID:27073735

  8. Identification of monoclinic calcium pyrophosphate dihydrate and hydroxyapatite in human sclera using Raman microspectroscopy

    PubMed Central

    Chen, Ko-Hua; Li, Mei-Jane; Cheng, Wen-Ting; Balic-Zunic, Tonci; Lin, Shan-Yang

    2009-01-01

    Raman microspectroscopy was first used to determine the composition of a calcified plaque located at the pterygium-excision site of a 51-year-old female patient's left nasal sclera after surgery. It was unexpectedly found that the Raman spectrum of the calcified sample at 1149, 1108, 1049, 756, 517, 376 and 352/cm was similar to the Raman spectrum of monoclinic form of calcium pyrophosphate dihydrate (CPPD) crystal, but differed from the Raman spectrum of triclinic form of CPPD. An additional peak at 958/cm was also observed in the Raman spectrum of the calcified plaque, which was identical to the characteristic peak at 958/cm of hydroxyapatite (HA). This is the first study to report the spectral biodiagnosis of both monoclinic CPPD and HA co-deposited in the calcified plaque of a patient with sclera dystrophic calcification using Raman microspectroscopy. PMID:19200254

  9. SRX - a X-ray spectroscopy beamline with sub-100nm spatial resolution at NSLS-II

    NASA Astrophysics Data System (ADS)

    Thieme, J.

    2011-12-01

    J. Thieme, V. deAndrade, Y. Yao, J. Prietzel* (NSLS-II, Brookhaven National Laboratory, USA; *TU Munich, Germany) The new electron storage ring NSLS-II will be a source of synchrotron radiation with an unmatched low emittance. Such a facility is very well suited for hosting experiments in need of coherent radiation. One of first six beamlines to be constructed at NSLS-II will be a high resolution spectroscopy station, dedicated especially for environmental and geo-sciences. A canted setup of two undulators will serve as independent light sources for two branches of this beamline. One branch line is planned to address the energy range from 4.65 keV to 24 keV focusing the beam down to a small spot size with Kirkpatrick-Baez mirrors. The expected photon flux in the spot is in the range of above 10^13 phot/sec. A horizontally deflecting double crystal monochromator with maximum stability will ensure the possibility of spectroscopy with very high spectral resolution. The second branch is planned for reaching lower X-ray energies, addressing the range of 2 keV up to 15 keV, but with a higher spatial resolution. Using a Fresnel zoneplate, the spatial resolution aimed for is in the range of 30 nm. It can be expected that this branch would be attractive for more biological applications from environmental science due to the many elements of interest within that energy range. The experimental station will be designed to not only host X-ray fluorescence experiments but diffraction imaging experiments as well. The commissioning of this beamline will start in 2014, therefore a detailed design description will be presented here. As an example of what is achievable at this NSLS-II beamline we will present a spatially resolved study on the co-localization of iron and sulfur in a forest soil. The scientific topic to be addressed was to identify unambiguously the relationship between the speciation of iron and sulfur as a function of the chemical state of the surrounding soil when

  10. Comparison of coherent and spontaneous Raman microspectroscopies for noninvasive detection of single bacterial endospores

    PubMed Central

    Petrov, Georgi I.; Arora, Rajan; Yakovlev, Vladislav V.; Wang, Xi; Sokolov, Alexei V.; Scully, Marlan O.

    2007-01-01

    Single bacterial spores were analyzed by using nonlinear Raman microspectroscopy based on coherent anti-Stokes Raman scattering (CARS). The Raman spectra were retrieved from CARS spectra and found to be in excellent agreement with conventionally collected Raman spectra. The phase retrieval method based on maximum entropy model revealed significant robustness to external noise. The direct comparison of signal amplitudes exhibited a factor of 100 stronger CARS signal, as compared with the Raman signal. PMID:17483468

  11. The characterisation of pluripotent and multipotent stem cells using Fourier transform infrared microspectroscopy.

    PubMed

    Cao, Julie; Ng, Elizabeth S; McNaughton, Donald; Stanley, Edouard G; Elefanty, Andrew G; Tobin, Mark J; Heraud, Philip

    2013-08-26

    Fourier transform infrared (FTIR) microspectroscopy shows potential as a benign, objective and rapid tool to screen pluripotent and multipotent stem cells for clinical use. It offers a new experimental approach that provides a holistic measurement of macromolecular composition such that a signature representing the internal cellular phenotype is obtained. The use of this technique therefore contributes information that is complementary to that acquired by conventional genetic and immunohistochemical methods.

  12. FOURIER TRANSFORM INFRARED MICROSPECTROSCOPY AS A TOOL TO IDENTIFY MACROALGAL PROPAGULES(1).

    PubMed

    Bellgrove, Alecia; Kihara, Hiroshi; Iwata, Akira; Aoki, Masakazu N; Heraud, Philip

    2009-06-01

    Understanding of macroalgal dispersal has been hindered by the difficulty in identifying propagules. Different carrageenans typically occur in gametophytes and tetrasporophytes of the red algal family Gigartinaceae, and we may expect that carpospores and tetraspores also differ in composition of carrageenans. Using Fourier transform infrared (FT-IR) microspectroscopy, we tested the model that differences in carrageenans and other cellular constituents between nuclear phases should allow us to discriminate carpospores and tetraspores of Chondrus verrucosus Mikami. Spectral data suggest that carposporophytes isolated from the pericarp and female gametophytes contained κ-carrageenan, whereas tetrasporophytes contained λ-carrageenan. However, both carpospores and tetraspores exhibited absorbances in wave bands characteristic of κ-, ι-, and λ-carrageenans. Carpospores contained more proteins and may be more photosynthetically active than tetraspores, which contained more lipid reserves. We draw analogies to planktotrophic and lecithotrophic larvae. These differences in cellular chemistry allowed reliable discrimination of spores, but pretreatment of spectral data affected the accuracy of classification. The best classification of spores was achieved with extended multiplicative signal correction (EMSC) pretreatment using partial least squares discrimination analysis, with correct classification of 86% of carpospores and 83% of tetraspores. Classification may be further improved by using synchrotron FT-IR microspectroscopy because of its inherently higher signal-to-noise ratio compared with microspectroscopy using conventional sources of IR. This study demonstrates that FT-IR microspectroscopy and bioinformatics are useful tools to advance our understanding of algal dispersal ecology through discrimination of morphologically similar propagules both within and potentially between species. © 2009 Phycological Society of America.

  13. The Characterisation of Pluripotent and Multipotent Stem Cells Using Fourier Transform Infrared Microspectroscopy

    PubMed Central

    Cao, Julie; Ng, Elizabeth S.; McNaughton, Donald; Stanley, Edouard G.; Elefanty, Andrew G.; Tobin, Mark J.; Heraud, Philip

    2013-01-01

    Fourier transform infrared (FTIR) microspectroscopy shows potential as a benign, objective and rapid tool to screen pluripotent and multipotent stem cells for clinical use. It offers a new experimental approach that provides a holistic measurement of macromolecular composition such that a signature representing the internal cellular phenotype is obtained. The use of this technique therefore contributes information that is complementary to that acquired by conventional genetic and immunohistochemical methods. PMID:24065090

  14. In vivo diffuse reflectance micro-spectroscopy for correction of Raman depth profiles acquired on skin

    NASA Astrophysics Data System (ADS)

    Roig, Blandine; Koenig, Anne; Perraut, François; Piot, Olivier; Manfait, Michel; Dinten, Jean-Marc

    2016-04-01

    Confocal Raman microspectroscopy is a relevant and useful tool to perform in vivo diagnosis of cutaneous tissues noninvasively and without labeling. This optical technique provides in-depth molecular and conformational characterization of skin. Unfortunately, spectral distortions occur due to elastic scattering. Our objective is to correct the attenuation of in-depth Raman peaks intensity by considering elastic scattering in biological tissues. In this purpose, a correction model was constructed using skin scattering properties as parameters thus enabling quantitative analysis. The work presented here is a technique of in vivo Diffuse Reflectance Micro-Spectroscopy called Micro-DRS. It achieves optical properties characterization in the skin layers probed by Raman microspectroscopy. The Micro-DRS setup can easily be coupled to a confocal Raman micro-probe to perform simultaneous measurements. Thanks to Monte Carlo simulations and experimental results obtained on homemade solid phantoms mimicking skin optical properties, we show that it is possible to measure the absorption coefficient μa, the reduced scattering coefficient μs', the scattering coefficient μs and the anisotropy of scattering g with this new apparatus. The measured scattering properties can be used subsequently as parameters in our correction model. Coupled to a Raman micro-spectrometer, Micro-DRS enables a quantitative analysis when tracking drug penetration through skin and it can be used independently to provide additional diagnosing criterions.

  15. Classification of Gemcitabine resistant Cholangiocarcinoma cell lines using synchrotron FTIR microspectroscopy.

    PubMed

    Wongwattanakul, Molin; Hahnvajanawong, Chariya; Tippayawat, Patcharaporn; Chio-Srichan, Sirinart; Leelayuwat, Chanvit; Limpaiboon, Temduang; Jearanaikoon, Patcharee; Heraud, Philip

    2017-03-01

    Cholangiocarcinoma (CCA), a cancer of bile duct epithelium, is a major health problem in Thailand especially in the northeast. Overall treatment outcomes have not shown much improvement because the disease is usually detected at an advanced stage and often shows chemotherapeutic resistance. High-throughput Fourier Transform Infrared (FTIR) microspectroscopy can be used for cell classification and has the potential to diagnose cancer and possibly predict chemo-response. This study was aimed to differentiate gemcitabine-sensitive and gemcitabine-resistant induction in two CCA cell lines (KKU-M139 and KKU-M214) and xenograft tissues using synchrotron-FTIR microspectroscopy. Partial Least Squares Discriminant Analysis (PLS-DA) could discriminate between chemo-sensitive and chemo-resistant cells in the FTIR fingerprint spectral region (1800-1000 cm(-1) ) with more than 90% sensitivity and specificity. The chemo-resistant and chemo-sensitive phenotypes were different in protein (amide I, amide II), lipids (carbonyl group and CH3 deformation) and phosphodiester from nucleic acids. Additionally, spectra from xenograft tissues showed similar results to the cell line study with marked differences between chemo-resistant and chemo-sensitive CCA tissues, and PLS-DA could discriminate the chemotherapeutic response with 98% sensitivity and specificity. This is the first study to demonstrate the use of FTIR microspectroscopy to assess chemo-response both in vitro and in vivo. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Confocal Raman microspectroscopy of stratum corneum: a pre-clinical validation study.

    PubMed

    Wu, J; Polefka, T G

    2008-02-01

    Skin moisturization is not only important for maintaining skin functional properties but also has great impact on the skin's aesthetic properties. The top layer of the skin, the stratum corneum (SC), plays a key role in protecting and preventing against external aggressions as well as in regulating water flux in and out. Confocal Raman microspectroscopy is the first commercially available technique that provides a non-invasive, in vivo method to determine depth profiles of water concentration in the skin, however, in this case it was applied in an in vitro setting. As the first phase of validating the usefulness of confocal Raman microspectroscopy, we used porcine skin as a surrogate for human skin. Water concentration profiles were obtained using confocal Raman microspectroscopy from isolated pigskin SC and compared with that using the Karl Fischer titration method. The two methods correlated very well with a regression coefficient of 1.07 as well as a correlation coefficient, R(2) = 0.989, which demonstrated the consistency and accuracy of confocal Raman microspectroscopy for water concentration determination. To evaluate the instrument's response to different skin care/cleansing products, a wide range of products were tested to compare their skin moisturization ability. Among those tested were a lotion, commercial soap bar, syndet bar, traditional non-emollient shower gel (water, Sodium Laureth Ether Sulfate (SLES), cocamidopropyl betaine system) and emollient containing shower gel (water, sunflower oil, SLES, cocamidopropyl betaine, glycerin, petrolatum). The results were consistent with what was expected. The water content on skin treated with (A) lotion was significantly higher than the non-treated control; (B) syndet bar-treated skin had a significantly higher water content than soap-based bar-treated sites; (C) non-emollient shower gel washed sites were more moisturized than soap-based bar-treated samples; and (D) emollient shower gel-treated skin was

  17. Comparative Study of Breast Normal and Cancer Cells Using Coherent Anti-Stokes Raman Scattering Microspectroscopy Imaging

    NASA Astrophysics Data System (ADS)

    Lee, Jang Hyuk; Cho, Eun Hee; Shin, Sang-Mo; Oh, Myoung-kyu; Ko, Do-Kyeong

    2012-08-01

    A coherent anti-Stokes Raman scattering (CARS) microspectroscopy imaging system was developed using a femtosecond laser and a photonic crystal fiber (PCF). We separated resonant and non-resonant CARS signals in the time domain by the chirp of the PCF, and applied this system to compare live human breast normal and cancer cells. The CARS image and spectrum at C-H stretch vibration in lipid droplets could subsequently be used to differentiate cancer cells from normal cells, thereby confirming the potential of the CARS microspectroscopy imaging system as a diagnostic tool that allows the high-sensitivity, high-resolution, and fast detection of breast cancer.

  18. Effects of nilotinib on leukaemia cells using vibrational microspectroscopy and cell cloning.

    PubMed

    Siddique, M R; Rutter, A V; Wehbe, K; Cinque, G; Bellisola, G; Sulé-Suso, J

    2017-04-10

    Over the last few years, both synchrotron-based FTIR (S-FTIR) and Raman microspectroscopies have helped to better understand the effects of drugs on cancer cells. However, cancer is a mixture of cells with different sensitivity/resistance to drugs. Furthermore, the effects of drugs on cells produce both chemical and morphological changes, the latter could affect the spectra of cells incubated with drugs. Here, we successfully cloned sensitive and resistant leukaemia cells to nilotinib, a drug used in the management of leukaemia. This allowed both the study of a more uniform population and the study of sensitive and resistant cells prior to the addition of the drug with both S-FTIR and Raman microspectroscopies. The incubation with nilotinib produced changes in the S-FTIR and Raman spectra of both sensitive and resistant clones to nilotinib. Principal component analysis was able to distinguish between cells incubated in the absence or presence of the drug, even in the case of resistant clones. The latter would confirm that the spectral differences between the so-called resistant clonal cells prior to and after adding a drug might reside on those more or less sensitive cells that have been able to remain alive when they were collected to be studied with S-FTIR or Raman microspectroscopies. The data presented here indicate that the methodology of cell cloning can be applied to different types of malignant cells. This should facilitate the identification of spectral biomarkers of sensitivity/resistance to drugs. The next step would be a better assessment of sensitivity/resistance of leukaemia cells from patients which could guide clinicians to better tailor treatments to each individual patient.

  19. Nanoliter volume, high-resolution NMR microspectroscopy using a 60-micron planar microcoil.

    PubMed

    Stocker, J E; Peck, T L; Webb, A G; Feng, M; Magin, R L

    1997-11-01

    Previous studies demonstrated the feasibility of using 100-microns inner diameter planar spiral inductors (microcoils) as detectors in 1H nuclear magnetic resonance (NMR) microspectroscopy. However, high-resolution NMR applications were not possible due to poor spectral resolution and low signal-to-noise ratio (SNR). These limitations in performance have now been largely overcome by using a nonconductive liquid fluorocarbon (FC-43) to minimize the effects of susceptibility mismatch between materials, and by carefully optimizing the microcoil geometry for maximum SNR. In this study, liquid samples were loaded into a fused silica capillary (75-microns inner diameter, 147-microns outer diameter). The capillary was positioned 50 microns above a 3.5-turn microcoil so that approximately 1 nL of the sample was present in the sensitive region of the microcoil. The microcoil was fabricated on a gallium arsenide substrate with an inner diameter of 60 microns, an outer diameter of 200 microns, trace width of 10 microns, trace spacing of 10 microns, and trace height of 3 microns. At 5.9 T (250 MHz) in 1H-NMR microspectroscopy experiments using a spectral width of 1 kHz, 4096 sampled data points, and a recovery delay of 1 s, a SNR of 25 (per acquisition) and a spectral linewidth of less than 2 Hz were obtained from a sample of water. These results demonstrate that planar microcoils can be used for high-resolution NMR microspectroscopy. Such coils may also be suitable for localized NMR studies at the cellular level and as detectors in capillary electrophoresis or microbore liquid chromatography.

  20. Raman microspectroscopy for in situ examination of carbon-microbe-mineral interactions

    NASA Astrophysics Data System (ADS)

    Creamer, C.; Foster, A. L.; Lawrence, C. R.; Mcfarland, J. W.; Waldrop, M. P.

    2016-12-01

    The changing paradigm of soil organic matter formation and turnover is focused at the nexus of microbe-carbon-mineral interactions. However, visualizing biotic and abiotic stabilization of C on mineral surfaces is difficult given our current techniques. Therefore we investigated Raman microspectroscopy as a potential tool to examine microbially mediated organo-mineral associations. Raman microspectroscopy is a non-destructive technique that has been used to identify microorganisms and minerals, and to quantify microbial assimilation of 13C labeled substrates in culture. We developed a partial least squares regression (PLSR) model to accurately quantify (within 5%) adsorption of four model 12C substrates (glucose, glutamic acid, oxalic acid, p-hydroxybenzoic acid) on a range of soil minerals. We also developed a PLSR model to quantify the incorporation of 13C into E. coli cells. Using these two models, along with measures of the 13C content of respired CO2, we determined the allocation of glucose-derived C into mineral-associated microbial biomass and respired CO2 in situ and through time. We observed progressive 13C enrichment of microbial biomass with incubation time, as well as 13C enrichment of CO2 indicating preferential decomposition of glucose-derived C. We will also present results on the application of our in situ chamber to quantify the formation of organo-mineral associations under both abiotic and biotic conditions with a variety of C and mineral substrates, as well as the rate of turnover and stabilization of microbial residues. Application of Raman microspectroscopy to microbial-mineral interactions represents a novel method to quantify microbial transformation of C substrates and subsequent mineral stabilization without destructive sampling, and has the potential to provide new insights to our conceptual understanding of carbon-microbe-mineral interactions.

  1. Discrimination of functional hepatocytes derived from mesenchymal stem cells using FTIR microspectroscopy.

    PubMed

    Ye, Danna; Tanthanuch, Waraporn; Thumanu, Kanjana; Sangmalee, Anawat; Parnpai, Rangsun; Heraud, Philip

    2012-10-21

    Functional hepatocytes differentiated in vitro from mesenchymal stem cells (MSCs) need to be fully characterized before they could be applied as a therapy to treat liver disease. Here, we employed Fourier Transform Infrared (FTIR) microspectroscopy to investigate the characteristics of hepatocyte-like cells derived from rat bone marrow mesenchymal stem cells (rBM-MSCs) by detecting changes in macromolecular composition occurring during the hepatogenesis process. Partial Least Squares Discriminant Analysis (PLS-DA) enabled us to discriminate undifferentiated rBM-MSCs, and early, mid-stage and late stage rBM-MSCs derived hepatocytes by their characteristic FTIR "spectroscopic signatures". The predominant spectroscopic changes responsible for this discrimination were changes in FTIR absorbance bands at: 3012 cm(-1) (cis C[double bond, length as m-dash]C stretch from unsaturated lipids), 2952 cm(-1) (ν(as)CH(3) from lipids), 2854 cm(-1) (ν(s)CH(2) from lipids) and 1722 cm(-1) (C[double bond, length as m-dash]O stretching from lipids), which were associated with triglyceride and unsaturated fatty acid accumulation in the hepatocyte-like cells occurring during differentiation. Based on these findings, rBM-MSCs derived hepatocytes are characterized by high lipid content which facilitates a means of identifying hepatocytes from their stem cells progenitors by using FTIR microspectroscopy. Other complex changes in spectral bands assigned to proteins and nucleic acids were observed during hepatocyte differentiation indicating that mRNA translation was taking place producing proteins related to the formation of the new hepatocyte-like phenotype, which was corroborated by immunohistochemistry. The results show FTIR microspectroscopy combined with bioinformatic modeling constitutes a powerful new phenotypic-based methodology for monitoring and characterization of the process of stem cell differentiation leading to the formation of hepatocytes, providing complementary

  2. Phenotypic profiling of keloid scars using FT-IR microspectroscopy reveals a unique spectral signature.

    PubMed

    Hollywood, Katherine A; Maatje, Marlies; Shadi, Iqbal T; Henderson, Alex; McGrouther, Duncan Angus; Goodacre, Royston; Bayat, Ardeshir

    2010-12-01

    Keloid disease (KD) is a quasineoplastic fibroproliferative tumour of unknown origin causing a progressive, recurrent dermal lesion. KD is not homogeneous in nature and shows phenotypic structural differences between its distinct peripheral margins compared to its centre. The keloid margin is often symptomatically more active with increased dermal cellularity, compared to a symptomatically dormant and hypocellular centre of lesion. The aim of this study was to delineate the morphological components of a keloid scar tissue by measuring the differences between various anatomical locations within the keloid tissue, such as the margin and the centre of the lesion compared to its surrounding normal skin using Fourier transform infrared (FT-IR) microspectroscopy. FT-IR microspectroscopy is a technique that produces spectra with detailed molecular biochemical information inherent of the chemical structure. Chemical maps were constructed on extralesional cross sections taken from six keloid scars. H&E stained sections were used to confirm diagnosis of keloid and orientate the experimental cross sections prior to FT-IR. Spectral band assignment and principal components analysis were conducted. Distinct vibrational bands (100 spectra) were observed using FT-IR spectroscopy. Partial least squares discriminant analysis, with bootstrapping (10,000 analyses), identified whether a spectrum was from the keloid or normal tissue showing an average accuracy of 84.8%, precision of 80.4%, specificity of 76.2%, and sensitivity of 92.9%. FT-IR microspectroscopy showed significant differences in spectral profiles in keloid tissue in different anatomical locations within the cross section. We believe that this proof-of-concept study may help substantiate the use of FTIR spectroscopy in keloid diagnosis and prognosis.

  3. Infrared Microspectroscopy of Bionanomaterials (Diatoms) with Careful Evaluation of Void Effects.

    PubMed

    Alipour, Leila; Hamamoto, Mai; Nakashima, Satoru; Harui, Rika; Furiki, Masanari; Oku, Osamu

    2016-03-01

    In order to characterize a representative natural bionanomaterial, present day centric diatom samples (diameter, 175-310 µm) have been analyzed and imaged by infrared (IR) micro-spectroscopy and scanning electron microscopy (SEM). Because diatom silica frustules have complex microscopic morphology, including many void areas such as micro- or nano-pores, the effects of voids on the spectral band shapes were first evaluated. With increasing void area percentage, 1220 cm(-1)/1070 cm(-1) peak height ratio (Si-O polymerization index) increases and 950 cm(-1)/800 cm(-1) peak height ratio (Si-OH/Si-O-Si) decreases, both approaching 1. Based on the void area percentage of representative diatom samples determined using SEM image analyses (51.5% to 20.5%) and spectral simulation, the 1220 cm(-1)/1070 cm(-1) ratios of diatom samples are sometimes affected by the void effect, but the 950 cm(-1)/800 cm(-1) ratios can indicate real structural information of silica. This void effect should be carefully evaluated for IR micro-spectroscopy of micro-nano-porous materials. Maturity of diatom specimens may be evaluated from: (1) void area percentages determined by SEM; (2) average thicknesses determined by optical microscope; and (3) average values of 1220 cm(-1)/1070 cm(-1) peak height ratios (opposite trend to the void effect) determined by IR micro-spectroscopy. Microscopic heterogeneities of chemical structures of silica were obtained by IR micro-spectroscopic mapping of four representative diatoms. The 950 cm(-1)/800 cm(-1) ratios show that large regions of some diatoms consist of hydrated amorphous immature silica. The successful analysis of diatoms by IR micro-spectroscopic data with careful void effect evaluation may be applied to physicochemical structures of many other bionanomaterials.

  4. Analysis of bone protein and mineral composition in bone disease using synchrotron infrared microspectroscopy

    NASA Astrophysics Data System (ADS)

    Miller, Lisa M.; Hamerman, David; Chance, Mark R.; Carlson, Cathy S.

    1999-10-01

    Infrared (IR) microspectroscopy is an analytical technique that is highly sensitive to the chemical components in bone. The brightness of a synchrotron source permits the examination of individual regions of bone in situ at a spatial resolution superior to that of a conventional infrared source. At Beamlines U10B and U2B at the National Synchrotron Light Source, we are examining the role of bone chemical composition in bone disease. In osteoarthritis (OA), it has been demonstrated that the bone underlying the joint cartilage (subchondral bone) becomes thickened prior to cartilage breakdown. Using synchrotron infrared microspectroscopy, we have examined the chemical composition of the subchondral bone in histologically normal and OA monkeys. Results demonstrate that the subchondral bone of OA monkeys is significantly more mineralized than the normal bone, primarily due to an increase in carbonate concentration in the OA bone. High resolution analysis indicates that differences in carbonate content are uniform throughout the subchondral bone region, suggesting that high subchondral bone carbonate may be a marker for OA. Conversely, increases in phosphate content are more pronounced in the region near the marrow space, suggesting that, as the subchondral bone thickens, the bone also becomes more mineralized. Osteoporosis is a disease characterized by a reduction in bone mass and a skeleton that is more susceptible to fracture. To date, it is unclear whether bone remodeled after the onset of osteoporosis differs in chemical composition from older bone. Using fluorescence-assisted infrared microspectroscopy, we are comparing the composition of monkey bone remodeled at various time points after the onset of osteoporosis (induced by ovariectomy). We find that the chemical composition of bone remodeled one year after ovariectomy and one year prior to necropsy is similar to normal bone. On the other hand, bone remodeled two years after ovariectomy is less mature, indicated

  5. Detection of template binding to molecularly imprinted polymers by Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Kantarovich, Keren; Belmont, Anne-Sophie; Haupt, Karsten; Bar, Ilana; Gheber, Levi A.

    2009-05-01

    We report on sensitive and specific detection and quantification of a template in a molecularly imprinted polymer (MIP) using Raman microspectroscopy. The β-blocking drug S-propranolol and its enantiomer, R-propranolol, were used as target molecules since the selectivity of this MIP is well established and serves as an appropriate validation standard. Specific peaks originating in the template were identified in the Raman spectrum, allowing quantification of bound target molecule. We demonstrate that label-free monitoring can be achieved from volumes as small as 1 μm3 of MIP, based on a single identifying peak.

  6. A method for examining the chemical basis for bone disease: synchrotron infrared microspectroscopy.

    PubMed

    Miller, L M; Carlson, C S; Carr, G L; Chance, M R

    1998-02-01

    Infrared microspectroscopy combines microscopy and spectroscopy for the purpose of chemical microanalysis. Light microscopy provides a way to generate and record magnified images and visibly resolve microstructural detail. Infrared spectroscopy provides a means for analyzing the chemical makeup of materials. Combining light microscopy and infrared spectroscopy permits the correlation of microstructure with chemical composition. Inherently, the long wavelengths of infrared radiation limit the spatial resolution of the technique. However, synchrotron infrared radiation significantly improves both the spectral and spatial resolution of an infrared microspectrometer, such that data can be obtained with high signal-to-noise at the diffraction limit, which is 3-5 microm in the mid-infrared region. In this study, we use infrared microspectroscopy to study the chemical composition of bone using two mapping methods. In the osteon method, linear maps are collected from the center of an osteon (newer bone) to the periphery (older bone) and their chemical compositions are compared. In the transverse method, applied specifically to subchondral bone, line maps are collected from the edge of the articular cartilage (older bone) to the marrow space (newer bone). A significant advantage of infrared microspectroscopy over other chemical methods is that the bone does not need to be homogenized for testing; we are able to study cross-sectional samples of bone in situ at a resolution better than 5 microm and compare the results with morphological findings on stained serial sections immediately adjacent to those examined by infrared microspectroscopy. The infrared absorption bands of bone proteins and mineral are sensitive to mineral content (i.e. carbonate, phosphate, acid phosphate), mineral crystallinity and the content/nature of the organic matrix. In this study, they are analyzed as a function of (1) age, i.e. distance with respect to the center of an osteon, and (2) morphology, i

  7. Determination of phosphate phases in sewage sludge ash-based fertilizers by Raman microspectroscopy.

    PubMed

    Vogel, Christian; Adam, Christian; McNaughton, Don

    2013-09-01

    The chemical form of phosphate phases in sewage sludge ash (SSA)-based fertilizers was determined by Raman microspectroscopy. Raman mapping with a lateral resolution of 5 × 5 μm(2) easily detected different compounds present in the fertilizers with the help of recorded reference spectra of pure substances. Quartz and aluminosilicates showed Raman bands in the range of 450-520 cm(-1). Phosphates with apatite structure and magnesium triphosphate were determined at around 960 and 980 cm(-1), respectively. Furthermore, calcium/magnesium pyrophosphates were detected in some samples.

  8. Determination of phosphorus fertilizer soil reactions by Raman and synchrotron infrared microspectroscopy.

    PubMed

    Vogel, Christian; Adam, Christian; Sekine, Ryo; Schiller, Tara; Lipiec, Ewelina; McNaughton, Don

    2013-10-01

    The reaction mechanisms of phosphate-bearing mineral phases from sewage sludge ash-based fertilizers in soil were determined by Raman and synchrotron infrared microspectroscopy. Different reaction mechanisms in wet soil were found for calcium and magnesium (pyro-) phosphates. Calcium orthophosphates were converted over time to hydroxyapatite. Conversely, different magnesium phosphates were transformed to trimagnesium phosphate. Since the magnesium phosphates are unable to form an apatite structure, the plant-available phosphorus remains in the soil, leading to better growth results observed in agricultural pot experiments. The pyrophosphates also reacted very differently. Calcium pyrophosphate is unreactive in soil. In contrast, magnesium pyrophosphate quickly formed plant-available dimagnesium phosphate.

  9. One-step Real-time Food Quality Analysis by Simultaneous DSC-FTIR Microspectroscopy.

    PubMed

    Lin, Shan-Yang; Lin, Chih-Cheng

    2016-01-01

    This review discusses an analytical technique that combines differential scanning calorimetry and Fourier-transform infrared (DSC-FTIR) microspectroscopy, which simulates the accelerated stability test and detects decomposition products simultaneously in real time. We show that the DSC-FTIR technique is a fast, simple and powerful analytical tool with applications in food sciences. This technique has been applied successfully to the simultaneous investigation of: encapsulated squid oil stability; the dehydration and intramolecular condensation of sweetener (aspartame); the dehydration, rehydration and solidification of trehalose; and online monitoring of the Maillard reaction for glucose (Glc)/asparagine (Asn) in the solid state. This technique delivers rapid and appropriate interpretations with food science applications.

  10. Absorption microspectroscopy, theory and applications in the case of the photosynthetic compartment.

    PubMed

    Barsanti, Laura; Evangelista, Valtere; Frassanito, Anna Maria; Vesentini, Nicoletta; Passarelli, Vincenzo; Gualtieri, Paolo

    2007-01-01

    We performed microspectroscopic evaluation of the pigment composition of the photosynthetic compartments of both algae and higher plants. The feasibility of microspectroscopy for discriminating among species and/or phylogenetic groups was tested on laboratory cultures. Gaussian bands decompositions, and a fitting algorithm, together with fourth-derivative transformation of absorbance spectra, provided a reliable discrimination among chlorophylls, phycobiliproteins and carotenoids. Comparative analysis of absorption spectra highlighted the evolutionary grouping of the algae into three main lineages in accordance with the most recent endosymbiotic theories.

  11. In vivo prediction of the nutrient status of individual microalgal cells using Raman microspectroscopy.

    PubMed

    Heraud, Philip; Beardall, John; McNaughton, Don; Wood, Bayden R

    2007-10-01

    An in vivo method for predicting the nutrient status of individual algal cells using Raman microspectroscopy is described. Raman spectra of cells using 780 nm laser excitation show enhanced bands mainly attributable to chlorophyll a and beta-carotene. The relative intensities of chlorophyll a and beta-carotene bands changed under nitrogen limitation, with chlorophyll a bands becoming less intense and beta-carotene bands more prominent. Although spectra from N-replete and N-starved cell populations varied, each distribution was distinct enough such that multivariate classification methods, such as partial least squares discriminant analysis, could accurately predict the nutrient status of the cells from the Raman spectral data.

  12. Imaging Local Chemical Microstructure of Germinated Wheat with Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Koc,H.; Wetzel, D.

    2008-01-01

    The spatial resolution enabled by in situ Fourier-transform infrared (FT-IR) microspectroscopy as predicted from our earlier report in Spectroscopy (1) is applied to localized chemical analysis in this vital biological process of seed germination. Germination includes several different biochemical and structural processes. Ultimately, the entire seed is consumed in sustaining the new life that results after sprouting and growth (2-4). Alpha amylase production is the standard evidence for detection of sprouted (germinated) wheat at harvest. Moist preharvest conditions can cause devastating losses and render the harvested wheat unfit for flour production. Dormancy of dry seeds following harvest retards sprouting under proper storage.

  13. Coherent anti-Stokes Raman microspectroscopy using spectral focusing with glass dispersion

    SciTech Connect

    Rocha-Mendoza, Israel; Langbein, Wolfgang; Borri, Paola

    2008-11-17

    We demonstrate experimentally that coherent anti-Stokes Raman microspectroscopy with high spectral resolution is achieved using femtosecond laser pulses chirped up to a few picoseconds by glass elements of known group-velocity dispersion without significant intensity losses. By simply choosing the length of the glass, the chirp of Stokes and pump pulses is tailored to obtain a spectral resolution given by the Fourier limit of the chirped pulse duration. We show that for chirped pulse durations shorter than or comparable to the Raman coherence time, maximum signal occurs for a pump arriving after the Stokes pulse, a time-ordering effect confirmed by numerical simulations.

  14. Cryogenic Field Measurement of Pr2Fe14B Undulator and Performance Enhancement Options at the NSLS-II

    SciTech Connect

    Tanabe, T.; Chubar, O.; Harder, David A.; Lehecka, Michael; Rank, James; Rakowsky, George; Spataro, Charles

    2009-09-27

    Short period (14.5mm) hybrid undulator arrays composed of Praseodymium Iron Boron (Pr{sub 2}Fe{sub 14}B) magnets (CR53, NEOMAX, Inc.) and vanadium permendur poles have been fabricated at Brookhaven National Laboratory. Unlike Neodymium Iron Boron (Nd{sub 2}Fe{sub 14}B) magnets which exhibit spin reorientation at temperatures below 150K, PrFeB arrays monotonically increase performance with lower operating temperature. It opens up the posibility for use in operating a cryo-permanent magnet undulator (CPMU) in the range of 40K to 60K where very efficient cryocoolers are available. Magnetic flux density profiles were measured at various temperature ranges from room temperature down to liquid helium (LHe) using the Vertical Testing Facility (VTF) at the National Snchrotron Light Source-II (NSLS-II). Temperature variations of phase error have been characterized. In addition, we examined the use of textured Dysprosium (Dy) poles to replace permendur poles to obtain further improvement in performance.

  15. Novel Method for Differentiating Histological Types of Gastric Adenocarcinoma by Using Confocal Raman Microspectroscopy.

    PubMed

    Hsu, Chih-Wei; Huang, Chia-Chi; Sheu, Jeng-Horng; Lin, Chia-Wen; Lin, Lien-Fu; Jin, Jong-Shiaw; Chau, Lai-Kwan; Chen, Wenlung

    2016-01-01

    Gastric adenocarcinoma, a single heterogeneous disease with multiple epidemiological and histopathological characteristics, accounts for approximately 10% of cancers worldwide. It is categorized into four histological types: papillary adenocarcinoma (PAC), tubular adenocarcinoma (TAC), mucinous adenocarcinoma (MAC), and signet ring cell adenocarcinoma (SRC). Effective differentiation of the four types of adenocarcinoma will greatly improve the treatment of gastric adenocarcinoma to increase its five-year survival rate. We reported here the differentiation of the four histological types of gastric adenocarcinoma from the molecularly structural viewpoint of confocal Raman microspectroscopy. In total, 79 patients underwent laparoscopic or open radical gastrectomy during 2008-2011: 21 for signet ring cell carcinoma, 21 for tubular adenocarcinoma, 14 for papillary adenocarcinoma, 6 for mucinous carcinoma, and 17 for normal gastric mucosas obtained from patients underwent operation for other benign lesions. Clinical data were retrospectively reviewed from medical charts, and Raman data were processed and analyzed by using principal component analysis (PCA) and linear discriminant analysis (LDA). Two-dimensional plots of PCA and LDA clearly demonstrated that the four histological types of gastric adenocarcinoma could be differentiated, and confocal Raman microspectroscopy provides potentially a rapid and effective method for differentiating SRC and MAC from TAC or PAC.

  16. Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis.

    PubMed

    Kumar, Srividya; Verma, Taru; Mukherjee, Ria; Ariese, Freek; Somasundaram, Kumaravel; Umapathy, Siva

    2016-04-07

    Biomolecular structure elucidation is one of the major techniques for studying the basic processes of life. These processes get modulated, hindered or altered due to various causes like diseases, which is why biomolecular analysis and imaging play an important role in diagnosis, treatment prognosis and monitoring. Vibrational spectroscopy (IR and Raman), which is a molecular bond specific technique, can assist the researcher in chemical structure interpretation. Based on the combination with microscopy, vibrational microspectroscopy is currently emerging as an important tool for biomedical research, with a spatial resolution at the cellular and sub-cellular level. These techniques offer various advantages, enabling label-free, biomolecular fingerprinting in the native state. However, the complexity involved in deciphering the required information from a spectrum hampered their entry into the clinic. Today with the advent of automated algorithms, vibrational microspectroscopy excels in the field of spectropathology. However, researchers should be aware of how quantification based on absolute band intensities may be affected by instrumental parameters, sample thickness, water content, substrate backgrounds and other possible artefacts. In this review these practical issues and their effects on the quantification of biomolecules will be discussed in detail. In many cases ratiometric analysis can help to circumvent these problems and enable the quantitative study of biological samples, including ratiometric imaging in 1D, 2D and 3D. We provide an extensive overview from the recent scientific literature on IR and Raman band ratios used for studying biological systems and for disease diagnosis and treatment prognosis.

  17. Identification of Pyridinoline Trivalent Collagen Cross-Links by Raman Microspectroscopy.

    PubMed

    Gamsjaeger, Sonja; Robins, Simon P; Tatakis, Dimitris N; Klaushofer, Klaus; Paschalis, Eleftherios P

    2017-02-28

    Intermolecular cross-linking of bone collagen is intimately related to the way collagen molecules are arranged in a fibril, imparts certain mechanical properties to the fibril, and may be involved in the initiation of mineralization. Raman microspectroscopy allows the analysis of minimally processed bone blocks and provides simultaneous information on both the mineral and organic matrix (mainly type I collagen) components, with a spatial resolution of ~1 μm. The aim of the present study was to validate Raman spectroscopic parameters describing one of the major mineralizing type I trivalent cross-links, namely pyridinoline (PYD). To achieve this, a series of collagen cross-linked peptides with known PYD content (as determined by HPLC analysis), human bone, porcine skin, predentin and dentin animal model tissues were analyzed by Raman microspectroscopy. The results of the present study confirm that it is feasible to monitor PYD trivalent collagen cross-links by Raman spectroscopic analysis in mineralized tissues, exclusively through a Raman band ~1660 wavenumbers. This allows determination of the relative PYD content in undecalcified bone tissues with a spatial resolution of ~1 μm, thus enabling correlations with histologic and histomorphometric parameters.

  18. Using Brillouin microspectroscopy to characterize adipocytes' response to lipid droplet accumulation

    NASA Astrophysics Data System (ADS)

    Troyanova-Wood, Maria; Coker, Zachary; Traverso, Andrew; Yakovlev, Vladislav V.

    2017-02-01

    Obesity and overweight are accompanied by an enlargement of adipocytes, which is commonly related to the increasing number or size of lipid droplets within the cells. Some studies have shown that the accumulation of lipid droplets within adipocytes results in their increased stiffness. Recently, Brillouin microspectroscopy has been introduced as a nondestructive method of imaging the elasticity of cells. Unlike other imaging modalities, it is capable of assessing the elastic properties on both tissue- and cell levels. In this study, Brillouin spectroscopy was used to measure the elasticity changes in response to accumulation of lipid droplets within adipocyte during adipogenesis. The cell line used in the study is 3T3-L1, with chemically-induced differentiation from pre-adipocytes to mature adipocytes. The Brillouin shift measurements of the cells before and after differentiation indicate that the stiffness of adipocytes increases due to accumulation of lipid droplets. The results are in agreement with previous atomic force microscopy (AFM) nanoindentation studies. Brillouin microspectroscopy is a technique suitable for measuring the changes of elasticity of adipocytes in response to lipid droplet accumulation.

  19. Spectroscopic signature of mouse embryonic stem cell-derived hepatocytes using synchrotron Fourier transform infrared microspectroscopy

    NASA Astrophysics Data System (ADS)

    Thumanu, Kanjana; Tanthanuch, Waraporn; Ye, Danna; Sangmalee, Anawat; Lorthongpanich, Chanchao; Parnpai, Rangsun; Heraud, Philip

    2011-05-01

    Stem cell-based therapy for liver regeneration has been proposed to overcome the persistent shortage in the supply of suitable donor organs. A requirement for this to succeed is to find a rapid method to detect functional hepatocytes, differentiated from embryonic stem cells. We propose Fourier transform infrared (FTIR) microspectroscopy as a versatile method to identify the early and last stages of the differentiation process leading to the formation of hepatocytes. Using synchrotron-FTIR microspectroscopy, the means of identifying hepatocytes at the single-cell level is possible and explored. Principal component analysis and subsequent partial least-squares (PLS) discriminant analysis is applied to distinguish endoderm induction from hepatic progenitor cells and matured hepatocyte-like cells. The data are well modeled by PLS with endoderm induction, hepatic progenitor cells, and mature hepatocyte-like cells able to be discriminated with very high sensitivity and specificity. This method provides a practical tool to monitor endoderm induction and has the potential to be applied for quality control of cell differentiation leading to hepatocyte formation.

  20. Multiplex coherent anti-Stokes Raman scattering microspectroscopy for monitoring molecular structural change in biological samples

    NASA Astrophysics Data System (ADS)

    Ohta, Takayuki; Hashizume, Hiroshi; Takeda, Keigo; Ishikawa, Kenji; Ito, Masafumi; Hori, Masaru

    2014-10-01

    Biological applications employing non-equilibrium plasma processing has been attracted much attention. It is essential to monitor the changes in an intracellular structure of the cell during the plasma exposure. In this study, we have analyzed the molecular structure of biological samples using multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy. Two picosecond pulse lasers with fundamental (1064 nm) or the supercontinuum (460-2200 nm) were employed as a pump and Stokes beams of multiplex CARS microspectroscopy, respectively. The pump and the Stokes laser beams were collinearly overlapped and tightly focused into a sample using an objective lens of high numerical aperture. The CARS signal was collected by another microscope objective lens which is placed facing the first one. After passing through a short pass filter, the signal was dispersed by a polychromator, and was detected by a charge-coupled device camera. The sample was sandwiched by a coverslip and a glass bottom dish for the measurements and was placed on a piezo stage. The CARS signals of the quinhydrone crystal at 1655, 1584, 1237 and 1161 cm-1 were assigned to the C-C, C =O stretching, O-H and C-O stretching vibrational modes, respectively.

  1. Novel Method for Differentiating Histological Types of Gastric Adenocarcinoma by Using Confocal Raman Microspectroscopy

    PubMed Central

    Hsu, Chih-Wei; Huang, Chia-Chi; Sheu, Jeng-Horng; Lin, Chia-Wen; Lin, Lien-Fu; Jin, Jong-Shiaw; Chau, Lai-Kwan; Chen, Wenlung

    2016-01-01

    Gastric adenocarcinoma, a single heterogeneous disease with multiple epidemiological and histopathological characteristics, accounts for approximately 10% of cancers worldwide. It is categorized into four histological types: papillary adenocarcinoma (PAC), tubular adenocarcinoma (TAC), mucinous adenocarcinoma (MAC), and signet ring cell adenocarcinoma (SRC). Effective differentiation of the four types of adenocarcinoma will greatly improve the treatment of gastric adenocarcinoma to increase its five-year survival rate. We reported here the differentiation of the four histological types of gastric adenocarcinoma from the molecularly structural viewpoint of confocal Raman microspectroscopy. In total, 79 patients underwent laparoscopic or open radical gastrectomy during 2008–2011: 21 for signet ring cell carcinoma, 21 for tubular adenocarcinoma, 14 for papillary adenocarcinoma, 6 for mucinous carcinoma, and 17 for normal gastric mucosas obtained from patients underwent operation for other benign lesions. Clinical data were retrospectively reviewed from medical charts, and Raman data were processed and analyzed by using principal component analysis (PCA) and linear discriminant analysis (LDA). Two-dimensional plots of PCA and LDA clearly demonstrated that the four histological types of gastric adenocarcinoma could be differentiated, and confocal Raman microspectroscopy provides potentially a rapid and effective method for differentiating SRC and MAC from TAC or PAC. PMID:27472385

  2. Evaluation of Bioreactor-Cultivated Bone by Magnetic Resonance Microscopy and FTIR Microspectroscopy

    PubMed Central

    Chesnick, Ingrid E.; Avallone, Frank; Leapman, Richard D.; Landis, William J.; Eidelman, Naomi; Potter, Kimberlee

    2007-01-01

    We present a three-dimensional mineralizing model based on a hollow fiber bioreactor (HFBR) inoculated with primary osteoblasts isolated from embryonic chick calvaria. Using non-invasive magnetic resonance microscopy (MRM), the growth and development of the mineralized tissue around the individual fibers were monitored over a period of nine weeks. Spatial maps of the water proton MRM properties of the intact tissue, with 78 μm resolution, were used to determine changes in tissue composition with development. Unique changes in the mineral and collagen content of the tissue were detected with high specificity by proton density (PD) and magnetization transfer ratio (MTR) maps, respectively. At the end of the growth period, the presence of a bone-like tissue was verified by histology and the formation of poorly crystalline apatite was verified by selected area electron diffraction and electron probe X-ray microanalysis. FTIR microspectroscopy confirmed the heterogeneous nature of the bone-like tissue formed. FTIR-derived phosphate maps confirmed that those locations with the lowest PD values contained the most mineral, and FTIR-derived collagen maps confirmed that bright pixels on MTR maps corresponded to regions of high collagen content. In conclusion, the spatial mapping of tissue constituents by FTIR microspectroscopy corroborated the findings of non-invasive MRM measurements and supported the role of MRM in monitoring the bone formation process in vitro. PMID:17174620

  3. Role of Synchrotron infra red microspectroscopy in studying epidermotropism of cutaneous T-cell lymphoma

    SciTech Connect

    El Bedewi, A.; El Anany, G; El Mofty, M

    2010-01-01

    The molecular mechanisms of epidermotropism in mycosis fungoides (MF) are not well understood to date. The aim of this study was to differentiate between epidermal and dermal lymphocytes within the skin of MF patients. This study was done on 10 MF patients with a mean age of 50 years diagnosed clinically in the Department of Dermatology, Cairo University, Egypt. A 6 mm biopsy was taken from each patient in order to confirm the diagnosis. Skin biopsies were cut, put on low e-slides and then stained with H&E. Further examination with Synchrotron infrared (IR) microspectroscopy was done in National Synchrotron Light Source - Brookhaven National Laboratory, New York, USA. Immunophenotyping using antibodies CD3, CD4, CD8, CD20 and CD30 was also done. Statistical analysis was done by Student's t-test and cluster analysis. Both epidermal and dermal lymphocytes were clustered separately. Also, Amide I and RNA and DNA within the lymphocytes were significantly different between the epidermis and the dermis. The biochemical analysis of protein, RNA and DNA with Synchrotron IR microspectroscopy is a promising tool for studying epidermotropism in cutaneous T-cell lymphoma.

  4. Surfactant uptake dynamics in mammalian cells elucidated with quantitative coherent anti-stokes Raman scattering microspectroscopy.

    PubMed

    Okuno, Masanari; Kano, Hideaki; Fujii, Kenkichi; Bito, Kotatsu; Naito, Satoru; Leproux, Philippe; Couderc, Vincent; Hamaguchi, Hiro-o

    2014-01-01

    The mechanism of surfactant-induced cell lysis has been studied with quantitative coherent anti-Stokes Raman scattering (CARS) microspectroscopy. The dynamics of surfactant molecules as well as intracellular biomolecules in living Chinese Hamster Lung (CHL) cells has been examined for a low surfactant concentration (0.01 w%). By using an isotope labeled surfactant having CD bonds, surfactant uptake dynamics in living cells has been traced in detail. The simultaneous CARS imaging of the cell itself and the internalized surfactant has shown that the surfactant molecules is first accumulated inside a CHL cell followed by a sudden leak of cytosolic components such as proteins to the outside of the cell. This finding indicates that surfactant uptake occurs prior to the cell lysis, contrary to what has been believed: surface adsorption of surfactant molecules has been thought to occur first with subsequent disruption of cell membranes. Quantitative CARS microspectroscopy enables us to determine the molecular concentration of the surfactant molecules accumulated in a cell. We have also investigated the effect of a drug, nocodazole, on the surfactant uptake dynamics. As a result of the inhibition of tubulin polymerization by nocodazole, the surfactant uptake rate is significantly lowered. This fact suggests that intracellular membrane trafficking contributes to the surfactant uptake mechanism.

  5. Demonstration of the Protein Involvement in Cell Electropermeabilization using Confocal Raman Microspectroscopy

    PubMed Central

    Azan, Antoine; Untereiner, Valérie; Gobinet, Cyril; Sockalingum, Ganesh D.; Breton, Marie; Piot, Olivier; Mir, Lluis M.

    2017-01-01

    Confocal Raman microspectroscopy was used to study the interaction between pulsed electric fields and live cells from a molecular point of view in a non-invasive and label-free manner. Raman signatures of live human adipose-derived mesenchymal stem cells exposed or not to pulsed electric fields (8 pulses, 1 000 V/cm, 100 μs, 1 Hz) were acquired at two cellular locations (nucleus and cytoplasm) and two spectral bands (600–1 800 cm−1 and 2 800–3 100 cm−1). Vibrational modes of proteins (phenylalanine and amide I) and lipids were found to be modified by the electropermeabilization process with a statistically significant difference. The relative magnitude of four phenylalanine peaks decreased in the spectra of the pulsed group. On the contrary, the relative magnitude of the amide I band at 1658 cm−1 increased by 40% when comparing pulsed and control group. No difference was found between the control and the pulsed group in the high wavenumber spectral band. Our results reveal the modification of proteins in living cells exposed to pulsed electric fields by means of confocal Raman microspectroscopy. PMID:28102326

  6. Spectroscopic signature of mouse embryonic stem cell-derived hepatocytes using synchrotron Fourier transform infrared microspectroscopy.

    PubMed

    Thumanu, Kanjana; Tanthanuch, Waraporn; Ye, Danna; Sangmalee, Anawat; Lorthongpanich, Chanchao; Parnpai, Rangsun; Heraud, Philip

    2011-05-01

    Stem cell-based therapy for liver regeneration has been proposed to overcome the persistent shortage in the supply of suitable donor organs. A requirement for this to succeed is to find a rapid method to detect functional hepatocytes, differentiated from embryonic stem cells. We propose Fourier transform infrared (FTIR) microspectroscopy as a versatile method to identify the early and last stages of the differentiation process leading to the formation of hepatocytes. Using synchrotron-FTIR microspectroscopy, the means of identifying hepatocytes at the single-cell level is possible and explored. Principal component analysis and subsequent partial least-squares (PLS) discriminant analysis is applied to distinguish endoderm induction from hepatic progenitor cells and matured hepatocyte-like cells. The data are well modeled by PLS with endoderm induction, hepatic progenitor cells, and mature hepatocyte-like cells able to be discriminated with very high sensitivity and specificity. This method provides a practical tool to monitor endoderm induction and has the potential to be applied for quality control of cell differentiation leading to hepatocyte formation.

  7. Characterisation of chondrogenic differentiation of human mesenchymal stem cells using synchrotron FTIR microspectroscopy.

    PubMed

    Chonanant, Chirapond; Jearanaikoon, Nichada; Leelayuwat, Chanvit; Limpaiboon, Temduang; Tobin, Mark J; Jearanaikoon, Patcharee; Heraud, Philip

    2011-06-21

    A major limiting factor in stem cell therapy is the accurate identification of the differentiation state of cells destined for transplantation. This study aimed to evaluate the potential of synchrotron radiation Fourier transform infrared (SR-FTIR) microspectroscopy as a novel technique to probe the differentiation state of human mesenchymal stem cells (hMSCs) to chondrocytes over a period of 7, 14 and 21 days of induction. The chondrogenic markers were determined using reverse transcription polymerase chain reaction, histology and immunohistochemistry. The changes of average spectra located near 1338-1230 and 1175-960 cm(-1) indicated increased levels of collagen and aggrecan, respectively, in chondrocyte-induced hMSCs compared with control cells. Classification of independent test spectra using partial least squares discriminant analysis (PLS-DA) could distinguish control and chondrocyte-induced cells with 100% accuracy. We conclude that the SR-FTIR microspectroscopy technique is sensitive for monitoring the differentiation state of stem cells under chondrogenic induction particularly at an early stage. It provides biochemical information that is complimentary to that obtained from conventional techniques, and may give more unambiguous results particularly at the very early stage of cellular differentiation. In addition, the spectroscopic approach is more straightforward, non-destructive and requires less sample preparation compared with the conventional methodologies.

  8. FT-IR microspectroscopy in rapid identification of bacteria in pure and mixed culture

    NASA Astrophysics Data System (ADS)

    Fontoura, Inglid; Belo, Ricardo; Sakane, Kumiko; Cardoso, Maria Angélica Gargione; Khouri, Sônia; Uehara, Mituo; Raniero, Leandro; Martin, Airton A.

    2010-02-01

    In recent years FT-IR microspectroscopy has been developed for microbiology analysis and applied successfully in pure cultures of microorganisms to rapidly identify strains of bacteria, yeasts and fungi. The investigation and characterization of microorganism mixed cultures is also of growing importance, especially in hospitals where it is common to poly-microbial infections. In this work, the rapid identification of bacteria in pure and mixed cultures was studied. The bacteria were obtained from the Institute Oswaldo Cruz culture collection at Brazil. Escherichia coli ATCC 10799 and Staphylococcus aureus ATCC 14456 were analyzed, 3 inoculations were examined in triplicate: Escherichia coli, Staphylococcus aureus and a mixed culture of them. The inoculations were prepared according to McFarland 0.5, incubated at 37 ° C for 6 hours, diluted in saline, placed in the CaF2 window and store for one hour at 50°C to obtain thin film. The measurement was performed by Spectrum Spotlight 400 (Perkin-Elmer) equipment in the range of 4000-900 cm-1, with 32 scans using a transmittance technique with point and image modes. The data were processed (baseline, normalization, calculation of first derivate followed by smoothing with 9 point using a Savitzky-Golay algorithm) and a cluster analysis were done by Ward's algorithm and an excellent discrimination between pure and mixed culture was obtained. Our preliminary results indicate that the FT-IR microspectroscopy associated with cluster analysis can be used to discriminate between pure and mixed culture.

  9. Aleurone Cell Walls of Wheat Grain: High Spatial Resolution Investigation Using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Jamme, F.; Robert, R; Bouchet, B; Saulnier, L; Dumas, P; Guillon, F

    2008-01-01

    Infrared microspectroscopy and immunolabeling techniques were employed in order to obtain deeper insight into the biochemical nature of aleurone cell walls of wheat grain. The use of a synchrotron source, thanks to its intrinsic brightness, has provided unprecedented information at the level of a few micrometers and has allowed the discrimination of various polysaccharides in cell walls. The high spectral quality obtained in the small analyzed domain has been beneficial in estimating the relative proportions of {Beta}-glucan and arabinoxylan, through the use of principal component analysis (PCA). The highest amount of {Beta}-glucan is found in periclinal cell walls close to the starchy endosperm. The junction regions between aleurone cells are enriched in arabinoxylan. At the early stage of wheat grain development (271 degrees D), the chemical composition along the cell walls is more heterogeneous than at the mature stage. Both synchrotron infrared microspectroscopy and immunolabeling experiments made it possible to reveal the spatial heterogeneity of the various chemical compositions of aleurone cell walls.

  10. Accurate and interpretable classification of microspectroscopy pixels using artificial neural networks.

    PubMed

    Manescu, Petru; Jong Lee, Young; Camp, Charles; Cicerone, Marcus; Brady, Mary; Bajcsy, Peter

    2017-04-01

    This paper addresses the problem of classifying materials from microspectroscopy at a pixel level. The challenges lie in identifying discriminatory spectral features and obtaining accurate and interpretable models relating spectra and class labels. We approach the problem by designing a supervised classifier from a tandem of Artificial Neural Network (ANN) models that identify relevant features in raw spectra and achieve high classification accuracy. The tandem of ANN models is meshed with classification rule extraction methods to lower the model complexity and to achieve interpretability of the resulting model. The contribution of the work is in designing each ANN model based on the microspectroscopy hypothesis about a discriminatory feature of a certain target class being composed of a linear combination of spectra. The novelty lies in meshing ANN and decision rule models into a tandem configuration to achieve accurate and interpretable classification results. The proposed method was evaluated using a set of broadband coherent anti-Stokes Raman scattering (BCARS) microscopy cell images (600 000  pixel-level spectra) and a reference four-class rule-based model previously created by biochemical experts. The generated classification rule-based model was on average 85% accurate measured by the DICE pixel label similarity metric, and on average 96% similar to the reference rules measured by the vector cosine metric. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Cold atmospheric-pressure plasma and bacteria: understanding the mode of action using vibrational microspectroscopy

    NASA Astrophysics Data System (ADS)

    Kartaschew, Konstantin; Baldus, Sabrina; Mischo, Meike; Bründermann, Erik; Awakowicz, Peter; Havenith, Martina

    2016-09-01

    Cold atmospheric-pressure plasma show promising antimicrobial effects, however the detailed biochemical mechanism of the bacterial inactivation is still unknown. We investigated, for the first time, plasma-treated Gram-positive Bacillus subtilis and Gram-negative Escherichia coli bacteria with Raman and infrared microspectroscopy. A dielectric barrier discharge was used as a plasma source. We were able to detect several plasma-induced chemical modifications, which suggest a pronounced oxidative effect on the cell envelope, cellular proteins and nucleotides as well as a generation of organic nitrates in the treated bacteria. Vibrational microspectroscopy is used as a comprehensive and a powerful tool for the analysis of plasma interactions with whole organisms such as bacteria. Analysis of reaction kinetics of chemical modifications allow a time-dependent insight into the plasma-mediated impact. Investigating possible synergistic effects between the plasma-produced components, our observations strongly indicate that the detected plasma-mediated chemical alterations can be mainly explained by the particle effect of the generated reactive species. By changing the polarity of the applied voltage pulse, and hence the propagation mechanisms of streamers, no significant effect on the spectral results could be detected. This method allows the analysis of the individual impact of each plasma constituent for particular chemical modifications. Our approach shows great potential to contribute to a better understanding of plasma-cell interactions.

  12. Uncovering the deactivation mechanism of Au catalyst with operando high spatial resolution IR and X-ray microspectroscopy measurements

    NASA Astrophysics Data System (ADS)

    Gross, Elad

    2016-06-01

    Detecting the reaction mechanism of multistep catalytic transformations is essential for optimization of these complex processes. In this study, the mechanism of catalyst deactivation within a flow reactor was studied under reaction conditions. Spectral mapping of the catalyst and the organic phase along a flow reactor were performed with micrometer-sized synchrotron-based X-ray and IR beams, respectively, with a spatial resolution of 15 μm. Heterogeneous Au catalyst was packed in a flow reactor and activated toward the cascade reaction of pyran formation. X-ray absorption microspectroscopy measurements revealed that the highly oxidized Au(III), which is the catalytically active species, was continuously reduced along the flow reactor. IR microspectroscopy measurements detected a direct correlation between the reduction of the Au catalyst and deactivation of the catalytic process. It was observed that within 1.5 mm from the reactor's inlet all the catalytic reactivity was quenched. Microspectroscopy measurements determined that the reduction of Au(III) was induced by nucleophilic attack of butanol, which is one of the reactants in this reaction. Slower deactivation rates were measured once the reactants concentration was decreased by an order of magnitude. Under these conditions the reaction path within the flow reactor was increased from 1.5 to 6 mm. These results demonstrate the molecular level understanding of reaction mechanism which can be achieved by high spatial resolution microspectroscopy measurements.

  13. Magnetic Field Mapping and Integral Transfer Function Matching of the Prototype Dipoles for the NSLS-II at BNL

    SciTech Connect

    He, P.; Jain, A., Gupta, R., Skaritka, J., Spataro, C., Joshi, P., Ganetis, G., Anerella, M., Wanderer, P.

    2011-03-28

    The National Synchrotron Light Source-II (NSLS-II) storage ring at Brookhaven National Laboratory (BNL) will be equipped with 54 dipole magnets having a gap of 35 mm, and 6 dipoles having a gap of 90 mm. Each dipole has a field of 0.4 T and provides 6 degrees of bending for a 3 GeV electron beam. The large aperture magnets are necessary to allow the extraction of long-wavelength light from the dipole magnet to serve a growing number of users of low energy radiation. The dipoles must not only have good field homogeneity (0.015% over a 40 mm x 20 mm region), but the integral transfer functions and integral end harmonics of the two types of magnets must also be matched. The 35 mm aperture dipole has a novel design where the yoke ends are extended up to the outside dimension of the coil using magnetic steel nose pieces. This design increases the effective length of the dipole without increasing the physical length. These nose pieces can be tailored to adjust the integral transfer function as well as the homogeneity of the integrated field. One prototype of each dipole type has been fabricated to validate the designs and to study matching of the two dipoles. A Hall probe mapping system has been built with three Group 3 Hall probes mounted on a 2-D translation stage. The probes are arranged with one probe in the midplane of the magnet and the others vertically offset by {+-}10 mm. The field is mapped around a nominal 25 m radius beam trajectory. The results of measurements in the as-received magnets, and with modifications made to the nose pieces are presented.

  14. MODULATION OF LOW ENERGY BEAM TO GENERATE PREDEFINED BUNCH TRAINS FOR THE NSLS-II TOP-OFF INJECTION

    SciTech Connect

    Wang, G.M.; Cheng, W.X.; Shaftan, T.; Fliller, R.; Heese, R.; Rose, J.

    2011-03-28

    The NSLS II linac will produce a bunch train, 80-150 bunches long with 2 ns bunch spacing. Having the ability to tailor the bunch train can lead to the smaller bunch to bunch charge variation in the storage ring. A stripline is planned to integrate into the linac baseline to achieve this tailoring. The stripline must have a fast field rise and fall time to tailor each bunch. The beam dynamics is minimally affected by including the extra space for the stripline. This paper discusses the linac beam dynamics with stripline, and the optimal design of the stripline. A stripline is to be integrated in the linac to match the storage ring uniform bunch charge requirement, which simplifies the gun pulser electronics and looses the edge uniform requirement. It is located at low energy to lower the stripline power supply requirement and limit the dumped electron radiation. By turning off the stripline, the beam dynamics through linac is comparable with the baseline design. More advanced ideas can be explored. If a DC corrector along with the stripline is used, the core bunch trains gets kick from the stripline while the head and the tail of bunch train just gets a DC kick. The stripline power supply waveform is a single flat top waveform with fast rise and drop and the pulse length is {approx}200 ns long or 100 bunches, which may be easier from the power supply view point. We are also considering the bunch by bunch charge manipulation to match the storage ring uniform bunch charge distribution requirement. By modulating the flat top waveform at 250 MHz with adjustable amplitude, each the bunch center is either at 45 degree or 135 degree. Only the head or tail of the bunch is trimmed out. Although each bunch center deviation from idea center is very different at low energy, it is gradually minimized with beam energy increase.

  15. Raman microspectroscopy of Hematoporphyrins. Imaging of the noncancerous and the cancerous human breast tissues with photosensitizers

    NASA Astrophysics Data System (ADS)

    Brozek-Pluska, B.; Kopec, M.

    2016-12-01

    Raman microspectroscopy combined with fluorescence were used to study the distribution of Hematoporphyrin (Hp) in noncancerous and cancerous breast tissues. The results demonstrate the ability of Raman spectroscopy to distinguish between noncancerous and cancerous human breast tissue and to identify differences in the distribution and photodegradation of Hematoporphyrin, which is a photosensitizer in photodynamic therapy (PDT), photodynamic diagnosis (PDD) and photoimmunotherapy (PIT) of cancer. Presented results show that Hematoporphyrin level in the noncancerous breast tissue is lower compared to the cancerous one. We have proved also that the Raman intensity of lipids and proteins doesn't change dramatically after laser light irradiation, which indicates that the PDT treatment destroys preferably cancer cells, in which the photosensitizer is accumulated. The specific subcellular localization of photosensitizer for breast tissues samples soaked with Hematoporphyrin was not observed.

  16. Development of scattering near-field optical microspectroscopy apparatus using an infrared synchrotron radiation source

    NASA Astrophysics Data System (ADS)

    Ikemoto, Yuka; Ishikawa, Michio; Nakashima, Satoru; Okamura, Hidekazu; Haruyama, Yuichi; Matsui, Shinji; Moriwaki, Taro; Kinoshita, Toyohiko

    2012-04-01

    We report the status of a scattering near-field microspectroscopy apparatus developed at SPring-8 using an infrared synchrotron radiation (IR-SR) source. It consists of a scattering type scanning near-field optical microscope and a Fourier transform infrared spectrometer. The IR-SR is used as a highly brilliant and broad-band IR source. This apparatus has potential for application in near-field spectroscopy with high spatial resolution beyond the diffraction limit. In order to eliminate background scatterings from the probe shaft and/or sample surface, we used higher harmonic demodulation method. The near-field spectra were observed by 2nd harmonic components using the lock-in detection. The spatial resolution of about 300 nm was achieved at around 1000 cm- 1 (10 μm wavelength).

  17. Tissue diagnosis using power-sharing multifocal Raman micro-spectroscopy and auto-fluorescence imaging

    PubMed Central

    Sinjab, Faris; Kong, Kenny; Gibson, Graham; Varma, Sandeep; Williams, Hywel; Padgett, Miles; Notingher, Ioan

    2016-01-01

    We describe a multifocal Raman micro-spectroscopy detection method based on a digital micromirror device, which allows for simultaneous “power-sharing” acquisition of Raman spectra from ad hoc sampling points. As the locations of the points can be rapidly updated in real-time via software control of a liquid-crystal spatial light modulator (LC-SLM), this technique is compatible with automated adaptive- and selective-sampling Raman spectroscopy techniques, the latter of which has previously been demonstrated for fast diagnosis of skin cancer tissue resections. We describe the performance of this instrument and show examples of multiplexed measurements on a range of test samples. Following this, we show the feasibility of reducing measurement time for power-shared multifocal Raman measurements combined with confocal auto-fluorescence imaging to provide guided diagnosis of tumours in human skin samples. PMID:27570692

  18. Raman microspectroscopy of algal lipid bodies: β-carotene as a volume sensor

    NASA Astrophysics Data System (ADS)

    Pilát, Zdenek; Bernatová, Silvie; Ježek, Jan; Šery, Mojmir; Samek, Ota; Zemánek, Pavel; Nedbal, Ladislav; Trtílek, Martin

    2012-02-01

    Advanced optical instruments are useful for analysis and manipulation of individual living cells and their internal structures. We have employed Raman microspectroscopic analysis for assessment of algal lipid body (LB) volume in vivo. Some algae contain β-carotene in high amounts in their LBs, including strains which are considered useful in biotechnology for lipid and pigment production. We have detected proportionality between the Raman vibrations of β-carotene and the LB volume. This finding may allow fast acquisition of LB volume approximation valuable e.g. for Raman microspectroscopy assisted cell sorting. We combine optical manipulation and analysis on a microfluidic platform in order to achieve fast, effective, and non-invasive sorting based on spectroscopic features of the individual living cells. The resultant apparatus could find its use in demanding biotechnological applications such as selection of rare natural mutants or artificially modified cells resulting from genetic manipulations.

  19. High-Performance Versatile Setup for Simultaneous Brillouin-Raman Microspectroscopy

    NASA Astrophysics Data System (ADS)

    Scarponi, F.; Mattana, S.; Corezzi, S.; Caponi, S.; Comez, L.; Sassi, P.; Morresi, A.; Paolantoni, M.; Urbanelli, L.; Emiliani, C.; Roscini, L.; Corte, L.; Cardinali, G.; Palombo, F.; Sandercock, J. R.; Fioretto, D.

    2017-07-01

    Brillouin and Raman scattering spectroscopy are established techniques for the nondestructive contactless and label-free readout of mechanical, chemical, and structural properties of condensed matter. Brillouin-Raman investigations currently require separate measurements and a site-matched approach to obtain complementary information from a sample. Here, we demonstrate a new concept of fully scanning multimodal microspectroscopy for simultaneous detection of Brillouin and Raman light scattering in an exceptionally wide spectral range, from fractions of GHz to hundreds of THz. It yields an unprecedented 150-dB contrast, which is especially important for the analysis of opaque or turbid media such as biomedical samples, and spatial resolution on a subcellular scale. We report the first applications of this new multimodal method to a range of systems, from a single cell to the fast reaction kinetics of a curing process, and the mechanochemical mapping of highly scattering biological samples.

  20. Darkfield microspectroscopy of nanostructures on silver tip-enhanced Raman scattering probes

    SciTech Connect

    Itoh, Tamitake; Yamamoto, Yuko S.; Suzuki, Toshiaki; Kitahama, Yasutaka; Ozaki, Yukihiro

    2016-01-11

    We report an evaluation method employing darkfield microspectroscopy for silver probes used in tip-enhanced Raman scattering (TERS). By adjusting the darkfield illumination, the diffracted light from the probe outlines disappears and the diffracted light from the surface nanostructures and tips of the probes appears as colorful spots. Scanning electron microscopy reveals that the spectral variations in these spots reflect the shapes of the surface nanostructures. The tip curvatures correlate to the spectral maxima of their spots. Temporal color changes in the spots indicate the deterioration due to the oxidation of the silver surfaces. These results show that the proposed method is useful for in situ evaluation of plasmonic properties of TERS probes.

  1. Three-dimensional nonlinear microspectroscopy and imaging of soft condensed matter.

    PubMed

    Yang, Shan; Wysolmerski, Robert B; Ganikhanov, Feruz

    2011-10-01

    We report on the realization of a sensitive microspectroscopy and imaging approach based on a three-color femtosecond coherent anti-Stokes Raman scattering (CARS) technique with high spectral, time, and spatial resolution. Independently tunable, high-repetition rate optical parametric oscillators were used to attain a dynamic range of 5 orders of magnitude for time-domain CARS signal. The attained sensitivity permitted tracing the decay of weak and structurally complex Raman active modes in soft condensed matter. Application of this approach to imaging of the biological specimen shows a great potential in quantitative characterization of live biological media with an ability to access inter- and intra-molecular interactions. © 2011 Optical Society of America

  2. Microchemical Structure of Soybean Seeds Revealed in Situ by Ultraspatially Resolved Synchrotron Fourier Transformed Infrared Microspectroscopy

    SciTech Connect

    Pietrzak,L.; Miller, S.

    2005-01-01

    The distribution of water in soybean seeds during imbibition varies with the chemical composition of the tissue. To understand the dynamics of imbibition, the proteins, lipids, and carbohydrates of the cotyledons and hilum region in mature soybean seeds were mapped using synchrotron Fourier transformed infrared microspectroscopy, based on characteristic peaks for each component: amide I at 1650 cm{sup -1} and amide II at 1550 cm{sup -1} for protein, lipid ester stretch at 1545 cm{sup -1}, and the region from 1200 to 900 cm{sup -1} for carbohydrates. The amount and configuration of the proteins varied across the cotyledon, as well as the amount of lipid and carbohydrate. It was found that protein distribution across the cotyledon is similar to water distribution during imbibition. The chemistry of the hilum region was also studied, as this is the point of water entry, and differences in the chemical composition of the tissues studied were observed.

  3. Mapping of Redox State of Mitochondrial Cytochromes in Live Cardiomyocytes Using Raman Microspectroscopy

    PubMed Central

    Brazhe, Nadezda A.; Treiman, Marek; Brazhe, Alexey R.; Find, Ninett L.; Maksimov, Georgy V.; Sosnovtseva, Olga V.

    2012-01-01

    This paper presents a nonivasive approach to study redox state of reduced cytochromes , and of complexes II and III in mitochondria of live cardiomyocytes by means of Raman microspectroscopy. For the first time with the proposed approach we perform studies of rod- and round-shaped cardiomyocytes, representing different morphological and functional states. Raman mapping and cluster analysis reveal that these cardiomyocytes differ in the amounts of reduced cytochromes , and . The rod-shaped cardiomyocytes possess uneven distribution of reduced cytochromes , and in cell center and periphery. Moreover, by means of Raman spectroscopy we demonstrated the decrease in the relative amounts of reduced cytochromes , and in the rod-shaped cardiomyocytes caused by H2O2-induced oxidative stress before any visible changes. Results of Raman mapping and time-dependent study of reduced cytochromes of complexes II and III and cytochrome in cardiomyocytes are in a good agreement with our fluorescence indicator studies and other published data. PMID:22957018

  4. Characterization and Application of a Grazing Angle Objective for Quantitative Infrared Reflection Microspectroscopy

    NASA Technical Reports Server (NTRS)

    Pepper, Stephen V.

    1995-01-01

    A grazing angle objective on an infrared microspectrometer is studied for quantitative spectroscopy by considering the angular dependence of the incident intensity within the objective's angular aperture. The assumption that there is no angular dependence is tested by comparing the experimental reflectance of Si and KBr surfaces with the reflectance calculated by integrating the Fresnel reflection coefficient over the angular aperture under this assumption. Good agreement was found, indicating that the specular reflectance of surfaces can straight-forwardly be quantitatively integrated over the angular aperture without considering non-uniform incident intensity. This quantitative approach is applied to the thickness determination of dipcoated Krytox on gold. The infrared optical constants of both materials are known, allowing the integration to be carried out. The thickness obtained is in fair agreement with the value determined by ellipsometry in the visible. Therefore, this paper illustrates a method for more quantitative use of a grazing angle objective for infrared reflectance microspectroscopy.

  5. Diagnosis of liver cancer from blood sera using FTIR microspectroscopy: a preliminary study.

    PubMed

    Thumanu, Kanjana; Sangrajrang, Suleeporn; Khuhaprema, Thiravud; Kalalak, Anant; Tanthanuch, Waraporn; Pongpiachan, Siwatt; Heraud, Philip

    2014-04-01

    FTIR microspectroscopy was applied for studying macromolecular changes in human serum samples from patients with healthy livers, and those diagnosed with liver cirrhosis or hepatocellular carcinoma (HCC). Our study demonstrated that the serum samples from HCC and cirrhotic patients could readily be discriminated from those from healthy controls based on macromolecular differences related to their lipid and protein structure. Spectral changes appeared to indicate that the secondary structure of protein from HCC sample groups contained a more distinctive β -sheet structure and a lower lipid content compared to samples from the healthy and cirrhosis group. This was correlated with measurements of large decreases in albumin levels in serum from diseased patients. We argue that this technique shows potential as a simple, rapid, inexpensive, and non-subjective methodology for the screening patients suspected of liver disease. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Synchrotron-based Infrared Microspectroscopy as a Useful Tool to Study Hydration States of Meteorite Constituents

    NASA Technical Reports Server (NTRS)

    Moroz, L. V.; Schmidt, M.; Schade, U.; Hiroi, T.; Ivanova, M. A.

    2005-01-01

    The meteorites Dho 225 and Dho 735 were recently found in Oman. Studies of their mineralogical and chemical composition suggest that these unusual meteorites are thermally metamorphosed CM2 chondrites [1,2,3]. Similar to Antarctic metamorphosed carbonaceous chondrites, the Dho 225 and Dho 735 are enriched in heavy oxygen compared to normal CMs [1,2]. However, IR studies indicating dehydration of matrix phyllosilicates are needed to confirm that the two new meteorites from Oman are thermally metamorphosed [4]. Synchrotron-based IR microspectroscopy is a new promising technique which allows the acquisition of IR spectra from extremely small samples. Here we demonstrate that this non-destructive technique is a useful tool to study hydration states of carbonaceous chondrites in situ. In addition, we acquired reflectance spectra of bulk powders of the Dho 225 and Dho 735 in the range of 0.3-50 microns.

  7. Synchrotron Infrared Microspectroscopy Study of Film Formation and Breakdown on Copper

    SciTech Connect

    Melendres, C. A.; Hahn, F.

    2010-02-03

    This work demonstrates the utility of synchrotron infrared reflectance microspectroscopy (SIRM), in the far and mid IR, for the determination of the composition of electrogenerated surface films formed during the general and localized corrosion of copper in bicarbonate solution. The back-reflection geometry was used. The anodic passivation film formed on copper at 0.2 V, in 0.01 M NaHCO{sub 3} solution consisted mainly of bicarbonate, copper carbonate dihydroxide or malachite [CuCO{sub 3}.Cu(OH){sub 2}], Cu(OH){sub 2}, and possibly some CuO. At higher potentials, the passive film breaks down and localized corrosion occurs leading to the formation of pits. The composition of the surface films inside the pits formed at 0.6 V was found to be essentially the same as that outside but the relative amount of Cu(OH){sub 2} is higher.

  8. Zirconia dental implants degradation by confocal Raman microspectroscopy: analytical simulation and experiments.

    PubMed

    Djaker, Nadia; Wulfman, Claudine; Sadoun, Michaël; Lamy de la Chapelle, Marc

    2013-05-01

    Subsurface hydrothermal degradation of yttria stabilized tetragonal zirconia polycrystals (3Y-TZP) is presented. Evaluation of low temperature degradation (LTD) phase transformation induced by aging in 3Y-TZP is experimentally studied by Raman confocal microspectroscopy. A non-linear distribution of monoclinic volume fraction is determined in depth by using different pinhole sizes. A theoretical simulation is proposed based on the convolution of the excitation intensity profile and the Beer-Lambert law (optical properties of zirconia) to compare between experiment and theory. The calculated theoretical degradation curves matche closely to the experimental ones. Surface transformation (V0) and transformation factor in depth (T) are obtained by comparing simulation and experience for each sample with nondestructive optical sectioning.

  9. Zirconia dental implants degradation by confocal Raman microspectroscopy: analytical simulation and experiments

    PubMed Central

    Djaker, Nadia; Wulfman, Claudine; Sadoun, Michaël; Lamy de la Chapelle, Marc

    2013-01-01

    Subsurface hydrothermal degradation of yttria stabilized tetragonal zirconia polycrystals (3Y-TZP) is presented. Evaluation of low temperature degradation (LTD) phase transformation induced by aging in 3Y-TZP is experimentally studied by Raman confocal microspectroscopy. A non-linear distribution of monoclinic volume fraction is determined in depth by using different pinhole sizes. A theoretical simulation is proposed based on the convolution of the excitation intensity profile and the Beer-Lambert law (optical properties of zirconia) to compare between experiment and theory. The calculated theoretical degradation curves matche closely to the experimental ones. Surface transformation (V0) and transformation factor in depth (T) are obtained by comparing simulation and experience for each sample with nondestructive optical sectioning. PMID:23667788

  10. Infrared micro-spectroscopy of strained VO2 micro-crystals

    NASA Astrophysics Data System (ADS)

    Qazilbash, M. M.; Huffman, T.; Walter, E. J.; Krakauer, H.; Wei, Jiang; Cobden, D. H.; Bechtel, H. A.; Martin, M. C.; Carr, G. L.; Basov, D. N.

    2012-02-01

    The temperature-driven insulator-to-metal transition (IMT) in vanadium dioxide (VO2) is accompanied by a structural instability (SI). The IMT and SI lead to a drastic change in the electronic properties, crystal structure, and lattice dynamics. We performed infrared micro-spectroscopy on single crystal platelets of VO2 deposited on oxidized silicon substrate by physical vapor deposition. The firm attachment of these micro-crystals to the substrate causes strain which can alter their properties compared to bulk samples. We report infrared data on these micro-crystals and demonstrate both their electronic and phonon properties in the monoclinic M1 phase and the rutile phase. We also compare their infrared conductivity to that of bulk single crystals and thin films. Finally, we compare infrared-active phonon features to first-principles density functional theory calculations.

  11. Analysis of coupled-bunch instabilities for the NSLS-II storage ring with a 500MHz 7-cell PETRA-III cavity

    SciTech Connect

    Bassi, G.; Blednykh, A.; Cheng, W.; Gao, F.; Rose, J.; Teytelman, D.

    2016-02-01

    The NSLS-II storage ring is designed to operate with superconducting RF-cavities with the aim to store an average current of 500 mA distributed in 1080 bunches, with a gap in the uniform filling for ion clearing. At the early stage of the commissioning (phase 1), characterized by a bare lattice without damping wigglers and without Landau cavities, a normal conducting 7-cell PETRA-III RF-cavity structure has been installed with the goal to store an average current of 25 mA. In this paper we discuss our analysis of coupled-bunch instabilities driven by the Higher Order Modes (HOMs) of the 7-cell PETRA-III RF-cavity. As a cure of the instabilities, we apply a well-known scheme based on a proper detuning of the HOMs frequencies based upon cavity temperature change, and the use of the beneficial effect of the slow head–tail damping at positive chromaticity to increase the transverse coupled-bunch instability thresholds. In addition, we discuss measurements of coupled-bunch instabilities observed during the phase 1 commissioning of the NSLS-II storage ring. In our analysis we rely, in the longitudinal case, on the theory of coupled-bunch instability for uniform fillings, while in the transverse case we complement our studies with numerical simulations with OASIS, a novel parallel particle tracking code for self-consistent simulations of collective effects driven by short and long-range wakefields.

  12. Analysis of coupled-bunch instabilities for the NSLS-II storage ring with a 500 MHz 7-cell PETRA-III cavity

    NASA Astrophysics Data System (ADS)

    Bassi, G.; Blednykh, A.; Cheng, W.; Gao, F.; Rose, J.; Teytelman, D.

    2016-02-01

    The NSLS-II storage ring is designed to operate with superconducting RF-cavities with the aim to store an average current of 500 mA distributed in 1080 bunches, with a gap in the uniform filling for ion clearing. At the early stage of the commissioning (phase 1), characterized by a bare lattice without damping wigglers and without Landau cavities, a normal conducting 7-cell PETRA-III RF-cavity structure has been installed with the goal to store an average current of 25 mA. In this paper we discuss our analysis of coupled-bunch instabilities driven by the Higher Order Modes (HOMs) of the 7-cell PETRA-III RF-cavity. As a cure of the instabilities, we apply a well-known scheme based on a proper detuning of the HOMs frequencies based upon cavity temperature change, and the use of the beneficial effect of the slow head-tail damping at positive chromaticity to increase the transverse coupled-bunch instability thresholds. In addition, we discuss measurements of coupled-bunch instabilities observed during the phase 1 commissioning of the NSLS-II storage ring. In our analysis we rely, in the longitudinal case, on the theory of coupled-bunch instability for uniform fillings, while in the transverse case we complement our studies with numerical simulations with OASIS, a novel parallel particle tracking code for self-consistent simulations of collective effects driven by short and long-range wakefields.

  13. Analysis of coupled-bunch instabilities for the NSLS-II storage ring with a 500MHz 7-cell PETRA-III cavity

    SciTech Connect

    Bassi, G.; Blednykh, A.; Cheng, W.; Gao, F.; Rose, J.; Teytelman, D.

    2015-12-11

    We present the NSLS-II storage ring that is designed to operate with superconducting RF-cavities with the aim to store an average current of 500 mA distributed in 1080 bunches, with a gap in the uniform filling for ion clearing. At the early stage of the commissioning (phase 1), characterized by a bare lattice without damping wigglers and without Landau cavities, a normal conducting 7-cell PETRA-III RF-cavity structure has been installed with the goal to store an average current of 25 mA. In this paper we discuss our analysis of coupled-bunch instabilities driven by the Higher Order Modes (HOMs) of the 7-cell PETRA-III RF-cavity. As a cure of the instabilities, we apply a well-known scheme based on a proper detuning of the HOMs frequencies based upon cavity temperature change, and the use of the beneficial effect of the slow head–tail damping at positive chromaticity to increase the transverse coupled-bunch instability thresholds. In addition, we discuss measurements of coupled-bunch instabilities observed during the phase 1 commissioning of the NSLS-II storage ring. In our analysis we rely, in the longitudinal case, on the theory of coupled-bunch instability for uniform fillings, while in the transverse case we complement our studies with numerical simulations with OASIS, a novel parallel particle tracking code for self-consistent simulations of collective effects driven by short and long-range wakefields.

  14. Raman Microspectroscopy of Individual Algal Cells: Sensing Unsaturation of Storage Lipids in vivo

    PubMed Central

    Samek, Ota; Jonáš, Alexandr; Pilát, Zdeněk; Zemánek, Pavel; Nedbal, Ladislav; Tříska, Jan; Kotas, Petr; Trtílek, Martin

    2010-01-01

    Algae are becoming a strategic source of fuels, food, feedstocks, and biologically active compounds. This potential has stimulated the development of innovative analytical methods focused on these microorganisms. Algal lipids are among the most promising potential products for fuels as well as for nutrition. The crucial parameter characterizing the algal lipids is the degree of unsaturation of the constituent fatty acids quantified by the iodine value. Here we demonstrate the capacity of the spatially resolved Raman microspectroscopy to determine the effective iodine value in lipid storage bodies of individual living algal cells. The Raman spectra were collected from three selected algal species immobilized in an agarose gel. Prior to immobilization, the algae were cultivated in the stationary phase inducing an overproduction of lipids. We employed the characteristic peaks in the Raman scattering spectra at 1,656 cm−1 (cis C═C stretching mode) and 1,445 cm−1 (CH2 scissoring mode) as the markers defining the ratio of unsaturated-to-saturated carbon-carbon bonds of the fatty acids in the algal lipids. These spectral features were first quantified for pure fatty acids of known iodine value. The resultant calibration curve was then used to calculate the effective iodine value of storage lipids in the living algal cells from their Raman spectra. We demonstrated that the iodine value differs significantly for the three studied algal species. Our spectroscopic estimations of the iodine value were validated using GC-MS measurements and an excellent agreement was found for the Trachydiscus minutus species. A good agreement was also found with the earlier published data on Botryococcus braunii. Thus, we propose that Raman microspectroscopy can become technique of choice in the rapidly expanding field of algal biotechnology. PMID:22163676

  15. Quantifying adhesive penetration in adhesive/dentin interface using confocal Raman microspectroscopy.

    PubMed

    Wang, Yong; Spencer, Paulette

    2002-01-01

    Confocal Raman microspectroscopy (CRM) provides an important and novel means of analyzing the chemical composition of the adhesive/dentin (a/d) interface. The purpose of this study was to develop a method for quantitative determination of the degree of adhesive penetration at the a/d interface using CRM. Three commercial dentin adhesive systems [Scotchbond Multipurpose Plus (SBMP+), Single Bond (SB), and Primer Bond NT (PBNT)] based on the total etch and "wet" bonding technique were examined in this study. Human dentin specimens treated with these adhesives were analyzed with CRM mapping across the a/d interface. Also, Raman spectra were collected on model mixtures of adhesive and type I collagen, and the ratios of the relative intensities of the Raman bands corresponding to adhesive and collagen were used for the construction of calibration curves. By comparing the Raman band ratios of interface specimens to the calibration curves, the percent of adhesive as a function of spatial position across the a/d interface was determined. The results show that there is a gradual decrease in penetration as a function of position for all three adhesive systems while the adhesive concentration gradient decreases in the order of SBMP+ > SB > PBNT. These differences in penetration of the three adhesives at the a/d interface also are discussed relative to the composition and phase segregation in adhesives. Additionally, our results indicate that confocal Raman microspectroscopy is a reliable in situ analytical technique for simple and rapid quantitative determination of adhesive penetration at its interface with prepared dentin. Copyright 2001 John Wiley & Sons, Inc.

  16. Raman microspectroscopy of individual algal cells: sensing unsaturation of storage lipids in vivo.

    PubMed

    Samek, Ota; Jonáš, Alexandr; Pilát, Zdeněk; Zemánek, Pavel; Nedbal, Ladislav; Tříska, Jan; Kotas, Petr; Trtílek, Martin

    2010-01-01

    Algae are becoming a strategic source of fuels, food, feedstocks, and biologically active compounds. This potential has stimulated the development of innovative analytical methods focused on these microorganisms. Algal lipids are among the most promising potential products for fuels as well as for nutrition. The crucial parameter characterizing the algal lipids is the degree of unsaturation of the constituent fatty acids quantified by the iodine value. Here we demonstrate the capacity of the spatially resolved Raman microspectroscopy to determine the effective iodine value in lipid storage bodies of individual living algal cells. The Raman spectra were collected from three selected algal species immobilized in an agarose gel. Prior to immobilization, the algae were cultivated in the stationary phase inducing an overproduction of lipids. We employed the characteristic peaks in the Raman scattering spectra at 1,656 cm(-1) (cis C═C stretching mode) and 1,445 cm(-1) (CH(2) scissoring mode) as the markers defining the ratio of unsaturated-to-saturated carbon-carbon bonds of the fatty acids in the algal lipids. These spectral features were first quantified for pure fatty acids of known iodine value. The resultant calibration curve was then used to calculate the effective iodine value of storage lipids in the living algal cells from their Raman spectra. We demonstrated that the iodine value differs significantly for the three studied algal species. Our spectroscopic estimations of the iodine value were validated using GC-MS measurements and an excellent agreement was found for the Trachydiscus minutus species. A good agreement was also found with the earlier published data on Botryococcus braunii. Thus, we propose that Raman microspectroscopy can become technique of choice in the rapidly expanding field of algal biotechnology.

  17. A Raman microspectroscopy study of water and trehalose in spin-dried cells.

    PubMed

    Abazari, Alireza; Chakraborty, Nilay; Hand, Steven; Aksan, Alptekin; Toner, Mehmet

    2014-11-18

    Long-term storage of desiccated nucleated mammalian cells at ambient temperature may be accomplished in a stable glassy state, which can be achieved by removal of water from the biological sample in the presence of glass-forming agents including trehalose. The stability of the glass may be compromised due to a nonuniform distribution of residual water and trehalose within and around the desiccated cells. Thus, quantification of water and trehalose contents at the single-cell level is critical for predicting the glass formation and stability for dry storage. Using Raman microspectroscopy, we estimated the trehalose and residual water contents in the microenvironment of spin-dried cells. Individual cells with or without intracellular trehalose were embedded in a solid thin layer of extracellular trehalose after spin-drying. We found strong evidence suggesting that the residual water was bound at a 2:1 water/trehalose molar ratio in both the extracellular and intracellular milieus. Other than the water associated with trehalose, we did not find any more residual water in the spin-dried sample, intra- or extracellularly. The extracellular trehalose film exhibited characteristics of an amorphous state with a glass transition temperature of ?22°C. The intracellular milieu also dried to levels suitable for glass formation at room temperature. These findings demonstrate a method for quantification of water and trehalose in desiccated specimens using confocal Raman microspectroscopy. This approach has broad use in desiccation studies to carefully investigate the relationship of water and trehalose content and distribution with the tolerance to drying in mammalian cells.

  18. Study of gemcitabine-sensitive/resistant cancer cells by cell cloning and synchrotron FTIR microspectroscopy.

    PubMed

    Rutter, Abigail V; Siddique, Muhammad R; Filik, Jacob; Sandt, Christophe; Dumas, Paul; Cinque, Gianfelice; Sockalingum, Ganesh D; Yang, Ying; Sulé-Suso, Josep

    2014-08-01

    Over the last few years, significant scientific insight on the effects of chemotherapy drugs at cellular level using synchrotron-based FTIR (S-FTIR) microspectroscopy has been obtained. The work carried out so far has identified spectral differences in cancer cells before and after the addition of drugs. However, this had to account for the following issues. First, chemotherapy agents cause both chemical and morphological changes in cells, the latter being responsible for changes in the spectral profile not correlated with biochemical characteristics. Second, as the work has been carried out in mixed populations of cells (resistant and sensitive), it is important to distinguish the spectral differences which are due to sensitivity/resistance to those due to cell morphology and/or cell mixture. Here, we successfully cloned resistant and sensitive lung cancer cells to a chemotherapy drug. This allowed us to study a more uniform population and, more important, allowed us to study sensitive and resistant cells prior to the addition of the drug with S-FTIR microscopy. Principal component analysis (PCA) did not detect major differences in resistant cells prior to and after adding the drug. However, PCA separated sensitive cells prior to and after the addition of the drug. This would indicate that the spectral differences between cells prior to and after adding a drug might reside on those more or less sensitive cells that have been able to remain alive when they were collected to be studied with S-FTIR microspectroscopy. This is a proof of concept and a feasibility study showing a methodology that opens a new way to identify the effects of drugs on more homogeneous cell populations using vibrational spectroscopy.

  19. Fourier transform infrared microspectroscopy shows significant differences between spectra of undifferentiated and polynucleated FLG 29.1 dried cells

    NASA Astrophysics Data System (ADS)

    Romano, Salvatore; Benvenuti, Susanna; Conti, Antonio; Benedetti, Enzo; Bramanti, Emilia; Rossi, Ilaria; Benedetti, Edoardo

    1994-02-01

    In a recent study made on cultures of human leukaemic cells (FLG 29.1 cell line) we were able to detect, by IR microspectroscopy, some significant IR spectroscopic variations following differentiation of cells towards osteoclastic-like behavior. The present study was undertaken on the same cell line in order to monitor biochemical structure variations following fusion induced by polyetilenglycole (PEG), using FTIR microspectroscopy. The finger-print region of all the spectra was retained and normalized according to a new regression procedure. Eleven bands were selected and total band power and mean power per unit frequency were compared with the corresponding reference session bands by a Dunnett's T test. Significant differences were found in both the tested variables only between treated and untreated cells, in 6 bands.

  20. Diagnosis of colon cancer by attenuated total reflectance-Fourier transform infrared microspectroscopy and soft independent modeling of class analogy.

    PubMed

    Khanmohammadi, Mohammadreza; Garmarudi, Amir Bagheri; Ghasemi, Keyvan; Jaliseh, Hadigheh Kazemi; Kaviani, Ahmad

    2009-01-01

    This study tries to demonstrate that attenuated total reflectance-fourier transform infrared (ATR-FTIR) microspectroscopy in combination with chemometric methods can reliably distinguish malignant colon tissues from healthy ones. It is important to explore a noninvasive and rapid method for detection of colon cancer biopsies. Initially, principal component analysis was applied to examine the degree of separation between tissue samples. Soft independent modeling of class analogy (SIMCA) was also employed to evaluate the prediction accuracy of ATR-FTIR microspectroscopy for the diagnosis of colon cancer. There were significant differences in the fourier transform infrared spectra of normal and cancerous colon biopsies in the 1,800-900 cm(-1) spectral region. The SIMCA results demonstrated that the accuracy, specificity, and sensitivity of the proposed diagnostic method were 93.3, 100, and 88.2%, respectively, which could help satisfy clinical diagnostic requirements.

  1. Application of linear discriminant analysis and Attenuated Total Reflectance Fourier Transform Infrared microspectroscopy for diagnosis of colon cancer.

    PubMed

    Khanmohammadi, Mohammadreza; Bagheri Garmarudi, Amir; Samani, Simin; Ghasemi, Keyvan; Ashuri, Ahmad

    2011-06-01

    Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) microspectroscopy was applied for detection of colon cancer according to the spectral features of colon tissues. Supervised classification models can be trained to identify the tissue type based on the spectroscopic fingerprint. A total of 78 colon tissues were used in spectroscopy studies. Major spectral differences were observed in 1,740-900 cm(-1) spectral region. Several chemometric methods such as analysis of variance (ANOVA), cluster analysis (CA) and linear discriminate analysis (LDA) were applied for classification of IR spectra. Utilizing the chemometric techniques, clear and reproducible differences were observed between the spectra of normal and cancer cases, suggesting that infrared microspectroscopy in conjunction with spectral data processing would be useful for diagnostic classification. Using LDA technique, the spectra were classified into cancer and normal tissue classes with an accuracy of 95.8%. The sensitivity and specificity was 100 and 93.1%, respectively.

  2. Fourier transform infrared microspectroscopy reveals unique phenotypes for human embryonic and induced pluripotent stem cell lines and their progeny.

    PubMed

    Cao, Julie; Ng, Elizabeth S; McNaughton, Don; Stanley, Edouard G; Elefanty, Andrew G; Tobin, Mark J; Heraud, Philip

    2014-10-01

    Fourier transform infrared (FTIR) microspectroscopy was employed to elucidate the macromolecular phenotype of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) and their differentiated progeny. Undifferentiated hESCs and hiPSC lines were found to be not clearly distinguishable from each other. However, although both hESC and hiPSC variants appeared to undergo similar changes during differentiation in terms of cell surface antigens, the derived cell types from all cell lines could be discriminated using FTIR spectroscopy. We foresee a possible future role for FTIR microspectroscopy as a powerful and objective investigative and quality control tool in regenerative medicine. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Monitoring secondary structural changes in salted and smoked salmon muscle myofiber proteins by FT-IR microspectroscopy.

    PubMed

    Carton, Izaskun; Böcker, Ulrike; Ofstad, Ragni; Sørheim, Oddvin; Kohler, Achim

    2009-05-13

    Fourier transform infrared (FT-IR) microspectroscopy and light microscopy were used to study changes in the myofibrillar proteins and microstructure in salmon muscle due to dry salting and smoking. Light microscopy showed that the myofibers of the smoked samples were more shrunken and their shape more irregular and edged than for the nonsmoked samples. FT-IR microspectroscopy showed that salting time mostly contributed in the amide I region, revealing that secondary structural changes of proteins were primarily affected by salting. The main variation in the amide II region was caused by smoking. As it is known that smoke components can react with amino acid side chains and that the contribution of the side chain in the amide II region is larger than that in amide I, it is concluded that the observed differences are due to interactions between carbonyl compounds of smoke and amino acid side chains.

  4. Perpendicular Magnetic Anisotropy in Ultrathin Co/Ni Multilayer Films Studies with Ferromagnetic Resonance and Magnetic X-Ray Microspectroscopy

    DTIC Science & Technology

    2012-06-28

    fields (approx 1 T) the Py magnetization will rotate out of the film plane and may effect the FMR measurement of the Co9Ni multilayer . However, no or...REPORT Perpendicular magnetic anisotropy in ultrathin Co|Ni multilayer films studied with ferromagnetic resonance and magnetic x-ray microspectroscopy...14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Ferromagnetic resonance ( FMR ) spectroscopy, x-ray magnetic circular dichroism (XMCD) spectroscopy and

  5. Red-shifted solitons for coherent anti-Stokes Raman scattering microspectroscopy in a polarization-maintaining photonic crystal fiber

    NASA Astrophysics Data System (ADS)

    Yuan, Jinhui; Sang, Xinzhu; Wu, Qiang; Zhou, Guiyao; Li, Feng; Yu, Chongxiu; Wang, Kuiru; Yan, Binbin; Han, Ying; Tam, Hwa Yaw; Wai, Ping-kong Alexander

    2015-05-01

    An alternative light source for coherent anti-Stokes Raman scattering (CARS) microspectroscopy based on red-shifted solitons in a polarization-maintaining photonic crystal fiber (PM-PCF) is experimentally demonstrated. By coupling femtosecond pulses into the anomalous dispersion region of the fundamental mode of a PM-PCF along the slow and fast axes, the red-shifted solitons generated can be used as the Stokes beams when the pump pulses are chosen as the pump beams. Through the process of red-shift, the frequency differences of the pump-Stokes beams are tunable in the ranges of 0 to 4068 cm-1 and 0 to 4594 cm-1, respectively. Moreover, because of the well maintained polarization states of the pump and Stokes beams and the high output powers of the solitons, CARS microspectroscopy using the proposed source will have a high signal-to-noise ratio and short data acquisition time. CARS microspectroscopy based on the proposed all-fiber light source can be used for studying a wide range of vibrational Raman spectra.

  6. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Wetzel, D.; Bonwell, E; Fritz, T; Fritz, A

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the {alpha}-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of {alpha}-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm{sup -1} was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}mX5{mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the {alpha}-helix population relative to other secondary protein structures from the position and shape of the amide I

  7. Determination of Endosperm Protein Secondary Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy

    SciTech Connect

    Bonwell,E.; Fisher, T.; Fritz, A.; Wetzel, D.

    2008-01-01

    One molecular aspect of mature hard wheat protein quality for breadmaking is the relative amount of endosperm protein in the a-helix form compared with that in other secondary structure forms including {beta}-sheet. Modeling of a-helix and {beta}-sheet absorption bands that contribute to the amide I band at 1650 cm-1 was applied to more than 1500 spectra in this study. The microscopic view of wheat endosperm is dominated by many large starch granules with protein in between. The spectrum produced from in situ microspectroscopy of this mixture is dominated by carbohydrate bands from the large starch granules that fill up the field. The high spatial resolution achievable with synchrotron infrared microspectroscopy enables revealing good in situ spectra of the protein located interstitially. Synchrotron infrared microspectroscopic mapping of 4 {mu}m thick frozen sections of endosperm in the subaleurone region provides spectra from a large number of pixels. Pixels with protein-dominated spectra are sorted out from among adjacent pixels to minimize the starch absorption and scattering contributions. Subsequent data treatment to extract information from the amide I band requires a high signal to noise ratio. Although spectral interference of the carbohydrate band on the amide band is not a problem, the scattering produced by the large starch granules diminishes the signal to noise ratio throughout the spectrum. High density mapping was done on beamlines U2B and U10B at the National Synchrotron Light Source at Brookhaven National Laboratory, Upton, NY. Mapping with a single masked spot size of 5.5 {mu}m diameter or confocal 5 {mu}m x 5 {mu}m spot size, respectively, on the two beamlines used produced spectra for new breeding lines under current consideration. Appropriate data treatment allows calculation of a numerical estimate of the a-helix population relative to other secondary protein structures from the position and shape of the amide I absorption band. Current

  8. Chemical Imaging on Liver Steatosis Using Synchrotron Infrared and ToF-SIMS Microspectroscopies

    PubMed Central

    Le Naour, François; Bralet, Marie-Pierre; Debois, Delphine; Sandt, Christophe; Guettier, Catherine; Dumas, Paul; Brunelle, Alain; Laprévote, Olivier

    2009-01-01

    Fatty liver or steatosis is a frequent histopathological change. It is a precursor for steatohepatitis that may progress to cirrhosis and in some cases to hepatocellular carcinoma. In this study we addressed the in situ composition and distribution of biochemical compounds on tissue sections of steatotic liver using both synchrotron FTIR (Fourier transform infrared) and ToF-SIMS (time of flight secondary ion mass spectrometry) microspectroscopies. FTIR is a vibrational spectroscopy that allows investigating the global biochemical composition and ToF-SIMS lead to identify molecular species in particular lipids. Synchrotron FTIR microspectroscopy demonstrated that bands linked to lipid contribution such as -CH3 and -CH2 as well as esters were highly intense in steatotic vesicles. Moreover, a careful analysis of the -CH2 symmetric and anti-symmetric stretching modes revealed a slight downward shift in spectra recorded inside steatotic vesicles when compared to spectra recorded outside, suggesting a different lipid environment inside the steatotic vesicles. ToF-SIMS analysis of such steatotic vesicles disclosed a selective enrichment in cholesterol as well as in diacylglycerol (DAG) species carrying long alkyl chains. Indeed, DAG C36 species were selectively localized inside the steatotic vesicles whereas DAG C30 species were detected mostly outside. Furthermore, FTIR detected a signal corresponding to olefin (C = C, 3000-3060 cm−1) and revealed a selective localization of unsaturated lipids inside the steatotic vesicles. ToF-SIMS analysis definitely demonstrated that DAG species C30, C32, C34 and C36 carrying at least one unsaturated alkyl chain were selectively concentrated into the steatotic vesicles. On the other hand, investigations performed on the non-steatotic part of the fatty livers have revealed important changes when compared to the normal liver. Although the non-steatotic regions of fatty livers exhibited normal histological aspect, IR spectra

  9. Photodiode-Based X-Ray Beam-Position Monitor With High Spatial-Resolution for the NSLS-II Beamlines

    SciTech Connect

    Yoon, P.S.; Siddons, D. P.

    2009-05-25

    We developed a photodiode-based monochromatic X-ray beam-position monitor (X-BPM) with high spatial resolution for the project beamlines of the NSLS-II. A ring array of 32 Si PIN-junction photodiodes were designed for use as a position sensor, and a low-noise HERMES4 ASIC chip was integrated into the electronic readout system. A series of precision measurements to characterize electrically the Si-photodiode sensor and the ASIC chip demonstrated that the inherent noise is sufficiently below tolerance levels. Following up modeling of detector's performance, including geometrical optimization using a Gaussian beam, we fabricated and assembled a first prototype. In this paper, we describe the development of this new state-of-the-art X-ray BPM along the beamline, in particular, downstream from the monochromator.

  10. Analysis of coupled-bunch instabilities for the NSLS-II storage ring with a 500MHz 7-cell PETRA-III cavity

    DOE PAGES

    Bassi, G.; Blednykh, A.; Cheng, W.; ...

    2015-12-11

    We present the NSLS-II storage ring that is designed to operate with superconducting RF-cavities with the aim to store an average current of 500 mA distributed in 1080 bunches, with a gap in the uniform filling for ion clearing. At the early stage of the commissioning (phase 1), characterized by a bare lattice without damping wigglers and without Landau cavities, a normal conducting 7-cell PETRA-III RF-cavity structure has been installed with the goal to store an average current of 25 mA. In this paper we discuss our analysis of coupled-bunch instabilities driven by the Higher Order Modes (HOMs) of themore » 7-cell PETRA-III RF-cavity. As a cure of the instabilities, we apply a well-known scheme based on a proper detuning of the HOMs frequencies based upon cavity temperature change, and the use of the beneficial effect of the slow head–tail damping at positive chromaticity to increase the transverse coupled-bunch instability thresholds. In addition, we discuss measurements of coupled-bunch instabilities observed during the phase 1 commissioning of the NSLS-II storage ring. In our analysis we rely, in the longitudinal case, on the theory of coupled-bunch instability for uniform fillings, while in the transverse case we complement our studies with numerical simulations with OASIS, a novel parallel particle tracking code for self-consistent simulations of collective effects driven by short and long-range wakefields.« less

  11. Imaging of Scleral Collagen Deformation Using Combined Confocal Raman Microspectroscopy and Polarized Light Microscopy Techniques

    PubMed Central

    Chakraborty, Nilay; Wang, Mian; Solocinski, Jason; Kim, Wonsuk; Argento, Alan

    2016-01-01

    This work presents an optospectroscopic characterization technique for soft tissue microstructure using site-matched confocal Raman microspectroscopy and polarized light microscopy. Using the technique, the microstructure of soft tissue samples is directly observed by polarized light microscopy during loading while spatially correlated spectroscopic information is extracted from the same plane, verifying the orientation and arrangement of the collagen fibers. Results show the response and orientation of the collagen fiber arrangement in its native state as well as during tensile and compressive loadings in a porcine sclera model. An example is also given showing how the data can be used with a finite element program to estimate the strain in individual collagen fibers. The measurements demonstrate features that indicate microstructural reorganization and damage of the sclera’s collagen fiber arrangement under loading. The site-matched confocal Raman microspectroscopic characterization of the tissue provides a qualitative measure to relate the change in fibrillar arrangement with possible chemical damage to the collagen microstructure. Tests and analyses presented here can potentially be used to determine the stress-strain behavior, and fiber reorganization of the collagen microstructure in soft tissue during viscoelastic response. PMID:27806070

  12. Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging

    DOE PAGES

    Lupoi, Jason S.; Smith-Moritz, Andreia; Singh, Seema; ...

    2015-07-10

    Background: Slow-degrading, fossil fuel-derived plastics can have deleterious effects on the environment, especially marine ecosystems. The production of bio-based, biodegradable plastics from or in plants can assist in supplanting those manufactured using fossil fuels. Polyhydroxybutyrate (PHB) is one such biodegradable polyester that has been evaluated as a possible candidate for relinquishing the use of environmentally harmful plastics. Results: PHB, possessing similar properties to polyesters produced from non-renewable sources, has been previously engineered in sugarcane, thereby creating a high-value co-product in addition to the high biomass yield. This manuscript illustrates the coupling of a Fourier-transform infrared microspectrometer, equipped with a focalmore » plane array (FPA) detector, with multivariate imaging to successfully identify and localize PHB aggregates. Principal component analysis imaging facilitated the mining of the abundant quantity of spectral data acquired using the FPA for distinct PHB vibrational modes. PHB was measured in the chloroplasts of mesophyll and bundle sheath cells, acquiescent with previously evaluated plant samples. Conclusion: This study demonstrates the power of IR microspectroscopy to rapidly image plant sections to provide a snapshot of the chemical composition of the cell. While PHB was localized in sugarcane, this method is readily transferable to other value-added co-products in different plants.« less

  13. Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging

    SciTech Connect

    Lupoi, Jason S.; Smith-Moritz, Andreia; Singh, Seema; McQualter, Richard; Scheller, Henrik V.; Simmons, Blake A.; Henry, Robert J.

    2015-07-10

    Background: Slow-degrading, fossil fuel-derived plastics can have deleterious effects on the environment, especially marine ecosystems. The production of bio-based, biodegradable plastics from or in plants can assist in supplanting those manufactured using fossil fuels. Polyhydroxybutyrate (PHB) is one such biodegradable polyester that has been evaluated as a possible candidate for relinquishing the use of environmentally harmful plastics. Results: PHB, possessing similar properties to polyesters produced from non-renewable sources, has been previously engineered in sugarcane, thereby creating a high-value co-product in addition to the high biomass yield. This manuscript illustrates the coupling of a Fourier-transform infrared microspectrometer, equipped with a focal plane array (FPA) detector, with multivariate imaging to successfully identify and localize PHB aggregates. Principal component analysis imaging facilitated the mining of the abundant quantity of spectral data acquired using the FPA for distinct PHB vibrational modes. PHB was measured in the chloroplasts of mesophyll and bundle sheath cells, acquiescent with previously evaluated plant samples. Conclusion: This study demonstrates the power of IR microspectroscopy to rapidly image plant sections to provide a snapshot of the chemical composition of the cell. While PHB was localized in sugarcane, this method is readily transferable to other value-added co-products in different plants.

  14. Determination of mechanical strength properties of hemp fibers using near-infrared fourier transform Raman microspectroscopy.

    PubMed

    Peetla, Padmaja; Schenzel, Karla C; Diepenbrock, Wulf

    2006-06-01

    Fourier transform near-infrared (FT-NIR) Raman microspectroscopy was adopted for analyzing the micro mechanical tensile deformation behavior of cellulosic plant fibers. Mechanical strength parameters such as tensile strength, failure strain, and Young's modulus of diversified hemp fibers were determined within the range of single fiber cells and fiber filaments. The analysis of fiber deformation at the molecular level was followed by the response of a characteristic Raman signal of fiber cellulose that is sensitive to the tensile load applied. The frequency shift of the Raman signal at 1095 cm(-1) to lower wavenumbers was observed when the fibers were subjected to tensile strain. Microstructural investigations using electron microscopy under environmental conditions supported the discussion of mechanical properties of hemp fibers in relation to several fiber variabilities. Generally, mechanical strength properties of diversified hemp fibers were discussed at the molecular, microstructural, and macroscale level. It was observed that mechanical strength properties of the fibers can be controlled in a broad range by appropriate mercerization parameters such as alkali concentration, fiber shrinkage, and tensile stress applied to the fibers during the alkaline treatments.

  15. Coexistence of probe conformations in lipid phases-a polarized fluorescence microspectroscopy study.

    PubMed

    Urbančič, Iztok; Ljubetič, Ajasja; Arsov, Zoran; Strancar, Janez

    2013-08-20

    Several well-established fluorescence methods depend on environment-sensitive probes that report about molecular properties of their local environment. For reliable interpretation of experiments, careful characterization of probes' behavior is required. In this study, bleaching-corrected polarized fluorescence microspectroscopy with nanometer spectral peak position resolution was applied to characterize conformations of two alkyl chain-labeled 7-nitro-2-1,3-benzoxadiazol-4-yl phospholipids in three model membranes, representing the three main lipid phases. The combination of polarized and spectral detection revealed two main probe conformations with their preferential fluorophore dipole orientations roughly parallel and perpendicular to membrane normal. Their peak positions were separated by 2-6 nm because of different local polarities and depended on lipid environment. The relative populations of conformations, estimated by a numerical model, indicated a specific sensitivity of the two probes to molecular packing with cholesterol. The coexistence of probe conformations could be further exploited to investigate membrane organization below microscopy spatial resolution, such as lipid rafts. With the addition of polarized excitation or detection to any environment-sensitive fluorescence imaging technique, the conformational analysis can be directly applied to explore local membrane complexity.

  16. Probing the whole ore chalcopyrite-bacteria interactions and jarosite biosynthesis by Raman and FTIR microspectroscopies.

    PubMed

    Adamou, Anastasia; Manos, Giorgos; Messios, Nicholas; Georgiou, Lazaros; Xydas, Constantinos; Varotsis, Constantinos

    2016-08-01

    The whole ore chalcopyrite-bacteria interaction and the formation of the extracellular polymeric substances (EPS) during the bioleaching process by microorganisms found in the mine of Hellenic Copper Mines in Cyprus were investigated. Raman and FTIR microspectroscopies have been applied towards establishing a direct method for monitoring the formation of secondary minerals and the newly found vibrational marker bands were used to monitor the time evolution of the formation of covellite, and the K(+) and NH4(+)-jarosites from the chalcopyrite surfaces. The Raman data indicate that the formation of K(+)-jarosite is followed by the formation of NH4(+)-jarosite. The variation in color in the FTIR imaging data and the observation of the amide I vibration at 1637cm(-1) indicate that the microorganisms are attached on the mineral surface and the changes in the frequency/intensity of the biofilm marker bands in the 900-1140cm(-1) frequency range with time demonstrate the existence of biofilm conformations.

  17. Using infrared and Raman microspectroscopies to compare ex vivo involved psoriatic skin with normal human skin

    NASA Astrophysics Data System (ADS)

    Leroy, Marie; Lefèvre, Thierry; Pouliot, Roxane; Auger, Michèle; Laroche, Gaétan

    2015-06-01

    Psoriasis is a chronic dermatosis that affects around 3% of the world's population. The etiology of this autoimmune pathology is not completely understood. The barrier function of psoriatic skin is known to be strongly altered, but the structural modifications at the origin of this dysfunction are not clear. To develop strategies to reduce symptoms of psoriasis or adequate substitutes for modeling, a deep understanding of the organization of psoriatic skin at a molecular level is required. Infrared and Raman microspectroscopies have been used to obtain direct molecular-level information on psoriatic and healthy human skin biopsies. From the intensities and positions of specific vibrational bands, the lipid and protein distribution and the lipid order have been mapped in the different layers of the skin. Results showed a similar distribution of lipids and collagen for normal and psoriatic human skin. However, psoriatic skin is characterized by heterogeneity in lipid/protein composition at the micrometer scale, a reduction in the definition of skin layer boundaries and a decrease in lipid chain order in the stratum corneum as compared to normal skin. A global decrease of the structural organization is exhibited in psoriatic skin that is compatible with an alteration of its barrier properties.

  18. Localization of polyhydroxybutyrate in sugarcane using Fourier-transform infrared microspectroscopy and multivariate imaging.

    PubMed

    Lupoi, Jason S; Smith-Moritz, Andreia; Singh, Seema; McQualter, Richard; Scheller, Henrik V; Simmons, Blake A; Henry, Robert J

    2015-01-01

    Slow-degrading, fossil fuel-derived plastics can have deleterious effects on the environment, especially marine ecosystems. The production of bio-based, biodegradable plastics from or in plants can assist in supplanting those manufactured using fossil fuels. Polyhydroxybutyrate (PHB) is one such biodegradable polyester that has been evaluated as a possible candidate for relinquishing the use of environmentally harmful plastics. PHB, possessing similar properties to polyesters produced from non-renewable sources, has been previously engineered in sugarcane, thereby creating a high-value co-product in addition to the high biomass yield. This manuscript illustrates the coupling of a Fourier-transform infrared microspectrometer, equipped with a focal plane array (FPA) detector, with multivariate imaging to successfully identify and localize PHB aggregates. Principal component analysis imaging facilitated the mining of the abundant quantity of spectral data acquired using the FPA for distinct PHB vibrational modes. PHB was measured in the chloroplasts of mesophyll and bundle sheath cells, acquiescent with previously evaluated plant samples. This study demonstrates the power of IR microspectroscopy to rapidly image plant sections to provide a snapshot of the chemical composition of the cell. While PHB was localized in sugarcane, this method is readily transferable to other value-added co-products in different plants.

  19. Darkfield reflection visible microspectroscopy equipped with a color mapping system of a brown altered granite.

    PubMed

    Onga, Chie; Nakashima, Satoru

    2014-01-01

    Visible darkfield reflectance spectroscopy equipped with a color mapping system has been developed and applied to a brown-colored Rokko granite sample. Sample reflectance spectra converted to Kubelka-Munk (KM) spectra show similar features to goethite and lepidocrocite. Raman microspectroscopy on the granite sample surface confirms the presence of these minerals. Here, L*a*b* color values (second Commission Internationale d'Eclairage [CIELab] 1976 color space) were determined from the sample reflection spectra. Grey, yellow, and brown zones of the granite show different L*, a*, and b* values. In the a*-b* diagram, a* and b* values in the grey and brown zones are on the lepidocrocite/ferrihydrite trends, but their values in the brown zone are larger than those in the grey zone. The yellow zone shows data points close to the goethite trend. Iron (hydr)oxide-rich areas can be visualized by means of large a* and b* values in the L*, a*, and b* maps. Although the present method has some problems and limitations, the visible darkfield reflectance spectroscopy can be a useful method for colored-material characterization.

  20. Decrease of aliphatic CHs from diatoms by in situ heating infrared microspectroscopy

    NASA Astrophysics Data System (ADS)

    Alipour, Leila; Nakashima, Satoru

    2016-04-01

    In situ heating IR microspectroscopy at 260-300°C under air and N2 conditions has been conducted on diatom frustules to examine aliphatic CH losses during heating, simulating their changes with burial-diagenesis. Assuming a reaction model made up of two first-order kinetic relations, reaction rate constants k1 and k2 and activation energies (Ea) were evaluated for aliphatic CHs. The rate constants for loss of aliphatic CHs of diatom frustules under air and N2 flow are much larger, with much smaller activation energies (57-109 kJ/mol: air; 14-44 kJ/mol: N2), than those for conventional hydrocarbon generation reactions from kerogens (170-370 kJ/mol) studied at higher temperatures (350-450°C). The CH decrease rates are somewhat different from the amide I decrease (protein degradation) rates. The obtained results suggest that organic transformation reactions including degradation of aliphatic CHs inside the diatom silica frustules might be quite different from those of kerogens separated from the biological structures.

  1. Nonlinear microspectroscopy in an optical tweezers system: application to cells marked with quantum dots

    NASA Astrophysics Data System (ADS)

    Fontes, Adriana; de Thomaz, Andre A.; Moreira, Wendel L.; Neves, Antonio A. R.; Barbosa, Luiz C.; de Farias, Patricia M. A.; Santos, Beate S.; Cesar, Carlos L.

    2005-03-01

    In this work we used our set up consisting of an optical tweezers plus non-linear micro-spectroscopy system to perform scanning microscopy and observe spectra using two photon excited (TPE) luminescence of captured single cells conjugated with quantum dots of CdS and CdTe. The CdS nanocrystals are obtained by our group via colloidal synthesis in aqueous medium with final pH = 7 using sodium polyphosphate as the stabilizing agent. In a second step the surface of CdS particles is functionalized with linking agents such as Glutaraldehyde. The CdTe quantum dots are functionalized in the its proper synthesis using mercaptoacetic acid (AMA). We used a femtosecond Ti:sapphire laser to excite the hyper Rayleigh or TPE luminescence in particles trapped with an Nd:YAG cw laser and a 30 cm monochromator equipped with a cooled back illuminated CCD to select the spectral region for imaging. With this system we obtained hyper Rayleigh and TPE luminescence images of macrophages and other samples. The results obtained show the potential presented by this system and fluorescent labels to perform spectroscopy in a living trapped microorganism in any neighbourhood and dynamically observe the chemical reactions changes in real time.

  2. In vitro colocalization of plasmonic nano-biolabels and biomolecules using plasmonic and Raman scattering microspectroscopy

    NASA Astrophysics Data System (ADS)

    Chaudhari, Kamalesh; Pradeep, Thalappil

    2015-04-01

    An insight into the intracellular fate of theranostics is important for improving their potential in biological applications. In vivo efficacy of plasmonic theranostics depends on our ability to monitor temporal changes in their size, shape, and state of aggregation, and the identification of molecules adsorbed on their surfaces. We develop a technique which combines plasmonic and Raman scattering microspectroscopy to colocalize plasmonic scattering from metallic nanoparticles with the Raman signatures of biomolecules adsorbed on the surface of the former. Using this technique, we have colocalized biomolecules with the plasmonic scattering from silver nanoparticles in the vicinity of Escherichia coli bacteria. To prove the applicability of this setup for the measurements on mammalian cells, imaging of HEK293 cells treated with gold nanoparticles was performed. We discuss the importance of such correlated measurements over individual techniques, although the latter may lead to misinterpretation of results. Finally, with the above-mentioned examples, we have given criteria to improve the specificity of theranostics. We believe that this methodology will be considered as a prime development in the assessment of theranostics.

  3. Infrared microspectroscopy analysis of ibuprofen release from drug eluting beads in uterine tissue.

    PubMed

    Namur, J; Wassef, M; Pelage, J P; Lewis, A; Manfait, M; Laurent, A

    2009-05-05

    Ibuprofen loaded embolization beads (IBU-BB) have been developed to reduce inflammation and pain following uterine artery embolization for the treatment of uterine fibroids. The present work has investigated the elution properties of IBU-BB in situ after embolization with Fourier Transform Infrared Microspectroscopy (FTIRMS). Twelve sheep underwent uterine artery embolization with IBU-BB (485 mM) or control unloaded beads. IBU concentration was determined inside the beads and in the tissue surrounding the beads using FTIRMS of uterine tissue sections sampled 24 h or 1 week after embolization. After 24 h, IBU concentration inside the bead was only 18.6 mM out of the 485 mM initially loaded (p < 0.0001, univariate sign test). The concentration in the tissue around the beads was 8 mM, which is well above the in vitro therapeutic levels (6 microM). After one week the concentration of IBU had decreased to 4.9 mM in the beads (p = 0.0502, Mann Whitney) and no IBU was detected in the surrounding tissue. This work has demonstrated that IBU-BB can provide a sustained release of the anti-inflammatory drug over at least one week. The in vivo elution properties of IBU-BB may be suitable to alleviate pain and inflammation after embolization.

  4. Classification of normal and malignant human gastric mucosa tissue with confocal Raman microspectroscopy and wavelet analysis

    NASA Astrophysics Data System (ADS)

    Hu, Yaogai; Shen, Aiguo; Jiang, Tao; Ai, Yong; Hu, Jiming

    2008-02-01

    Thirty-two samples from the human gastric mucosa tissue, including 13 normal and 19 malignant tissue samples were measured by confocal Raman microspectroscopy. The low signal-to-background ratio spectra from human gastric mucosa tissues were obtained by this technique without any sample preparation. Raman spectral interferences include a broad featureless sloping background due to fluorescence and noise. They mask most Raman spectral feature and lead to problems with precision and quantitation of the original spectral information. A preprocessed algorithm based on wavelet analysis was used to reduce noise and eliminate background/baseline of Raman spectra. Comparing preprocessed spectra of malignant gastric mucosa tissues with those of counterpart normal ones, there were obvious spectral changes, including intensity increase at ˜1156 cm -1 and intensity decrease at ˜1587 cm -1. The quantitative criterion based upon the intensity ratio of the ˜1156 and ˜1587 cm -1 was extracted for classification of the normal and malignant gastric mucosa tissue samples. This could result in a new diagnostic method, which would assist the early diagnosis of gastric cancer.

  5. The molecular structure and physical properties of elastin fibers as revealed by Raman microspectroscopy.

    PubMed

    Green, Ellen; Ellis, Richard; Winlove, Peter

    2008-11-01

    Raman microspectroscopy has been used to investigate the structure of alpha-elastin and fibrous elastin from ligament and aorta, and to explore changes associated with mechanical strain and temperature. Although no vibrational modes associated with cross-linking of the fibers could be identified, the secondary structure of dehydrated fibrous elastin was significantly different from alpha-elastin. The former differed from previous experimental measurements, but was close to the theoretical predictions with 36% beta-structures, 46% unordered, and 18% alpha-helix. Alpha-elastin contained 29% beta-structures, 53% unordered, and 18% alpha-helix. In nuchal fibers the amide I mode was polarized, consistent with the peptide bond. Strains of up to 60% in ligament fiber bundles resulted in no significant shifts in peak position or in secondary structure. Polarization measurements revealed that the peptide bonds and several side chains re-orientated closer to the fiber axis. Heating nuchal fibers to 60 degrees C to increase the energetic component of the elasticity was associated with a 30% increase in the proportion of beta-structures in the amide I band, a 50% increase in the amide III band, and a 50% reduction in the signal from bound water.

  6. Investigations of the supramolecular structure of individual diphenylalanine nano- and microtubes by polarized Raman microspectroscopy.

    PubMed

    Lekprasert, Banyat; Korolkov, Vladimir; Falamas, Alexandra; Chis, Vasile; Roberts, Clive J; Tendler, Saul J B; Notingher, Ioan

    2012-07-09

    Polarized Raman microspectroscopy and atomic force microscopy were used to obtain quantitative information regarding the molecular structure of individual diphenylalanine (FF) nano- and microtubes. The frequencies of the Raman spectral bands corresponding to the amide I (1690 cm(-1)) and amide III (1249 cm(-1)) indicated that the FF-molecules interact by hydrogen bonding at the N-H and not at the C═O sites. The calculated mean orientation angles of the principal axes of the Raman tensors (PARTs) obtained from the polarized Raman spectral measurements were 41 ± 4° for the amide I and 59 ± 5° for amide III. On the basis of the orientation of the PART for the amide I mode, it was found that the C═O bond is oriented at an angle of 8 ± 4° to the tube axis. These values did not vary significantly with the diameter of the tubes (range 400-1700 nm) and were in agreement with the molecular structure proposed previously for larger crystalline specimens.

  7. Quantification of chemotaxis-related alkane accumulation in Acinetobacter baylyi using Raman microspectroscopy.

    PubMed

    Li, Hanbing; L Martin, Francis Luke; Zhang, Dayi

    2017-03-03

    Alkanes are one of the most widespread contaminants in the natural environment, primarily as a consequence of biological synthesis and oil spills. Many indigenous microbes metabolize alkanes, and the chemotaxis and accumulation in some strains has been identified. For the first time, we apply Raman microspectroscopy to identify such chemotaxis-related affinity, and quantify the alkane concentrations via spectral alterations. Raman spectral alterations were only found for the alkane chemo-attractant bacteria Acinetobacter baylyi ADP1, not for Pseudomonas fluorescence, which exhibits limited chemotaxis towards alkane. The significant alterations were attributed to the strong chemotactic ability of A. baylyi enhancing the affinity and accumulation of alkane molecules on cell membranes or cellular internalization. Spectral fingerprints of A. baylyi significantly altered after 1-h exposure to pure alkanes (dodecane or tetradecane) and alkane mixtures (mineral oil or crude oil), but not monocyclic aromatic hydrocarbons (MAHs) or polycyclic aromatic hydrocarbons (PAHs). A semi-log linear regression relationship between Raman spectral alterations and alkane concentrations showed its feasibility in quantifying alkane concentration in environmental samples. Pure alkanes or alkane mixtures exhibited different limits of detection and regression slopes, indicating that the chemotaxis-related alkane accumulation in A. baylyi is dependent on the carbon chain length. This work provides a novel biospectroscopy approach to characterize the chemotaxis-related alkane bioaccumulation, and has immense potential for fast and high-throughput screening bacterial chemotaxis.

  8. Raman microspectroscopy discrimination of single human keratinocytes exposed at low dose of pesticide

    NASA Astrophysics Data System (ADS)

    Perna, Giuseppe; Lasalvia, Maria; Capozzi, Vito

    2012-02-01

    Raman spectroscopy is a useful technique for early diagnosis of cellular damage related to the exposure at toxic chemicals, because biochemical changes related to action mechanism of chemicals can be detected in Raman spectra. In this investigation Raman microspectroscopy has been used, in correlation with the principal component analysis method, to detect biochemical changes occurring in cultured human cells as a consequence of exposure at a commercial pesticide. Cultured human keratinocyte cells have been exposed at increasing concentrations of pesticide for 24 h. Viability tests indicated that the cells vitality is almost completely preserved when the concentration of active ingredient of pesticide is very low (5 × 10-8 M, about two orders of magnitude lower than the cytotoxic concentration at 24 h exposure). Nonetheless, the analysis of Raman spectra allows to state that a biochemical change occurs: it involves mainly the protein linkages between aminoacids (amide I bonds) and, at a minor amount, lipids. On the whole, principal components analysis is able to classify into two separate clusters the control and exposed human cells.

  9. Differentiating gastrointestinal stromal tumors from gastric adenocarcinomas and normal mucosae using confocal Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Hsu, Chih-Wei; Huang, Chia-Chi; Sheu, Jeng-Horng; Lin, Chia-Wen; Lin, Lien-Fu; Jin, Jong-Shiaw; Chen, Wenlung

    2016-07-01

    Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of the gastrointestinal tract, and gastric adenocarcinomas are a common cancer worldwide. To differentiate GISTs from adenocarcinomas is important because the surgical processes for both are different; the former excises the tumor with negative margins, while the latter requires radical gastrectomy with lymph node dissection. Endoscopy with biopsy is used to distinguish GISTs from adenocarcinomas; however, it may cause tumor bleeding in GISTs. We reported here the confocal Raman microspectroscopy as an effective tool to differentiate GISTs, adenocarcinomas, and normal mucosae. Of 119 patients enrolled in this study, 102 patients underwent gastrectomy (40 GISTs and 62 adenocarcinomas), and 17 patients with benign lesions were obtained as normal mucosae. Raman signals were integrated for 100 s for each spot on the specimen, and 5 to 10 spots, depending on the sample size, were chosen for each specimen. There were significant differences among those tissues as evidenced by different Raman signal responding to phospholipids and protein structures. The spectral data were further processed and analyzed by using principal component analysis. A two-dimensional plot demonstrated that GISTs, adenocarcinomas, and normal gastric mucosae could be effectively differentiated from each other.

  10. Identification of pigments in paint cross sections by reflection visible light imaging microspectroscopy.

    PubMed

    van der Weerd, Jaap; van Veen, Marieke K; Heeren, Ron M A; Boon, Jaap J

    2003-02-15

    A setup for reflection visible light imaging microspectroscopy (VIS-imaging) as well as its evaluation and application is described and tested. The spatial resolution of the system is approximately 1 microm at a spectral resolution of 4 nm. The optical contrast between different colored particles in the surface of a sample is optimized with a new image processing method for mapping of the distribution of the identified pigment particles. The potential of VIS-imaging in the study of paint cross sections obtained from paintings is explored. Spectra obtained from pigment particles in these cross sections result in classification or identification of several pigments. The investigated paint samples are challenging test cases, as they contain several colored materials with a very fine distribution. VIS-imaging can identify and map the most common traditional blue pigments, i.e., smalt, azurite, ultramarine, and indigo in 17th century oil paintings. Smalt can be identified even after complete discoloration. VIS-imaging analysis assisted in the identification and mapping of modern synthetic red and yellow pigments in a 20th century painting.

  11. In Situ FTIR Microspectroscopy of Brain Tissue from a Transgenic Mouse Model of Alzheimer Disease

    SciTech Connect

    Rak,M.; Del Bigio, M.; Mai, S.; Westaway, D.; Gough, K.

    2007-01-01

    Plaques composed of the A{beta} peptide are the main pathological feature of Alzheimer's disease. Dense-core plaques are fibrillar deposits of A{beta}, showing all the classical properties of amyloid including {beta}-sheet secondary structure, while diffuse plaques are amorphous deposits. We studied both plaque types, using synchrotron infrared (IR) microspectroscopy, a technique that allows the chemical composition and average protein secondary structure to be investigated in situ. We examined plaques in hippocampal, cortical and caudal tissue from 5- to 21-month-old TgCRND8 mice, a transgenic model expressing doubly mutant amyloid precursor protein, and displaying impaired hippocampal function and robust pathology from an early age. Spectral analysis confirmed that the congophilic plaque cores were composed of protein in a {beta}-sheet conformation. The amide I maximum of plaque cores was at 1623 cm-1, and unlike for in vitro A{beta} fibrils, the high-frequency (1680-1690 cm-1) component attributed to antiparallel {beta}-sheet was not observed. A significant elevation in phospholipids was found around dense-core plaques in TgCRND8 mice ranging in age from 5 to 21 months. In contrast, diffuse plaques were not associated with IR detectable changes in protein secondary structure or relative concentrations of any other tissue components.

  12. Using infrared and Raman microspectroscopies to compare ex vivo involved psoriatic skin with normal human skin.

    PubMed

    Leroy, Marie; Lefèvre, Thierry; Pouliot, Roxane; Auger, Michèle; Laroche, Gaétan

    2015-06-01

    Psoriasis is a chronic dermatosis that affects around 3% of the world's population. The etiology of this autoimmune pathology is not completely understood. The barrier function of psoriatic skin is known to be strongly altered, but the structural modifications at the origin of this dysfunction are not clear. To develop strategies to reduce symptoms of psoriasis or adequate substitutes for modeling, a deep understanding of the organization of psoriatic skin at a molecular level is required. Infrared and Raman microspectroscopies have been used to obtain direct molecular-level information on psoriatic and healthy human skin biopsies. From the intensities and positions of specific vibrational bands, the lipid and protein distribution and the lipid order have been mapped in the different layers of the skin. Results showed a similar distribution of lipids and collagen for normal and psoriatic human skin. However, psoriatic skin is characterized by heterogeneity in lipid/protein composition at the micrometer scale, a reduction in the definition of skin layer boundaries and a decrease in lipid chain order in the stratum corneum as compared to normal skin. A global decrease of the structural organization is exhibited in psoriatic skin that is compatible with an alteration of its barrier properties.

  13. Detecting viability transitions of umbilical cord mesenchymal stem cells by Raman micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Bai, H.; Chen, P.; Fang, H.; Lin, L.; Tang, G. Q.; Mu, G. G.; Gong, W.; Liu, Z. P.; Wu, H.; Zhao, H.; Han, Z. C.

    2011-01-01

    Recent research suggests that human umbilical cord derived mesenchymal stem cells (hUC-MSCs) can be promising candidates for cell-based therapy. Since large population and high viability are generally required, detecting viability transitions of these cells is crucial for their population expansion and quality control. Here, as a non-invasive method, Raman micro-spectroscopy is applied to examine hUC-MSCs with different viability. Using peak fitting and statistic t-test, the Raman peaks with obvious differences between the cells with high viability (> 90%) and low viability (< 20%) are extracted. It is found that the C=O out of plane bending in thymine at 744 cm-1, symmetric stretching of C-C in lipids at 877 cm-1 and CH deformation in proteins at 1342 cm-1 show the most significant changes (p < 0.001). When the cell viability decreases, the intensities of the former two peaks are both about doubled while that of the latter peak reduces by about 30%. Based on these results, we propose that the viability of hUC-MSCs can be characterized by these three peaks. And their intensity changes can be understood from the model of excessive reactive oxygen species interacting with the bio-macromolecules.

  14. Imaging of Scleral Collagen Deformation Using Combined Confocal Raman Microspectroscopy and Polarized Light Microscopy Techniques.

    PubMed

    Chakraborty, Nilay; Wang, Mian; Solocinski, Jason; Kim, Wonsuk; Argento, Alan

    2016-01-01

    This work presents an optospectroscopic characterization technique for soft tissue microstructure using site-matched confocal Raman microspectroscopy and polarized light microscopy. Using the technique, the microstructure of soft tissue samples is directly observed by polarized light microscopy during loading while spatially correlated spectroscopic information is extracted from the same plane, verifying the orientation and arrangement of the collagen fibers. Results show the response and orientation of the collagen fiber arrangement in its native state as well as during tensile and compressive loadings in a porcine sclera model. An example is also given showing how the data can be used with a finite element program to estimate the strain in individual collagen fibers. The measurements demonstrate features that indicate microstructural reorganization and damage of the sclera's collagen fiber arrangement under loading. The site-matched confocal Raman microspectroscopic characterization of the tissue provides a qualitative measure to relate the change in fibrillar arrangement with possible chemical damage to the collagen microstructure. Tests and analyses presented here can potentially be used to determine the stress-strain behavior, and fiber reorganization of the collagen microstructure in soft tissue during viscoelastic response.

  15. Multiphoton microscopy and microspectroscopy for diagnostics of inflammatory and neoplastic lung

    NASA Astrophysics Data System (ADS)

    Pavlova, Ina; Hume, Kelly R.; Yazinski, Stephanie A.; Flanders, James; Southard, Teresa L.; Weiss, Robert S.; Webb, Watt W.

    2012-03-01

    Limitations of current medical procedures for detecting early lung cancers inspire the need for new diagnostic imaging modalities for the direct microscopic visualization of lung nodules. Multiphoton microscopy (MPM) provides for subcellular resolution imaging of intrinsic fluorescence from unprocessed tissue with minimal optical attenuation and photodamage. We demonstrate that MPM detects morphological and spectral features of lung tissue and differentiates between normal, inflammatory and neoplastic lung. Ex vivo MPM imaging of intrinsic two-photon excited fluorescence was performed on mouse and canine neoplastic, inflammatory and tumor-free lung sites. Results showed that MPM detected microanatomical differences between tumor-free and neoplastic lung tissue similar to standard histopathology but without the need for tissue processing. Furthermore, inflammatory sites displayed a distinct red-shifted fluorescence compared to neoplasms in both mouse and canine lung, and adenocarcinomas displayed a less pronounced fluorescence emission in the 500 to 550 nm region compared to adenomas in mouse models of lung cancer. These spectral distinctions were also confirmed by two-photon excited fluorescence microspectroscopy. We demonstrate the feasibility of applying MPM imaging of intrinsic fluorescence for the differentiation of lung neoplasms, inflammatory and tumor-free lung, which motivates the application of multiphoton endoscopy for the in situ imaging of lung nodules.

  16. Synchrotron Infrared Reflectance Microspectroscopy Study of Film Formation and Breakdown on Copper

    SciTech Connect

    Hahn, F.; Melendres, C

    2010-01-01

    This work demonstrates the utility of synchrotron infrared reflectance microspectroscopy in the far- and mid-IR for the determination of the composition of electrogenerated surface films formed during the general and localized corrosion of copper in alkaline and bicarbonate solutions. Back-reflection geometry has been employed to identify the anodic film formed on copper in 0.1 M NaOH solution at 0.3 V (versus a Ag/AgCl reference) to be mainly CuO. In 0.01 M NaHCO{sub 3} solution general corrosion occurs with passive film formation below 0.2 V. The surface film at 0.2 V consisted mainly of bicarbonate, copper carbonate dihydroxide or malachite [CuCO{sub 3} {center_dot} Cu(OH){sub 2}], Cu(OH){sub 2} and possibly some CuO. At higher potentials the passive film breaks down and localized corrosion occurs leading to the formation of pits. The composition of the surface films inside the pits formed at 0.6 V was found to be essentially the same as that outside but the relative amount of Cu(OH){sub 2} appears to be higher.

  17. Development of Raman microspectroscopy for automated detection and imaging of basal cell carcinoma

    NASA Astrophysics Data System (ADS)

    Larraona-Puy, Marta; Ghita, Adrian; Zoladek, Alina; Perkins, William; Varma, Sandeep; Leach, Iain H.; Koloydenko, Alexey A.; Williams, Hywel; Notingher, Ioan

    2009-09-01

    We investigate the potential of Raman microspectroscopy (RMS) for automated evaluation of excised skin tissue during Mohs micrographic surgery (MMS). The main aim is to develop an automated method for imaging and diagnosis of basal cell carcinoma (BCC) regions. Selected Raman bands responsible for the largest spectral differences between BCC and normal skin regions and linear discriminant analysis (LDA) are used to build a multivariate supervised classification model. The model is based on 329 Raman spectra measured on skin tissue obtained from 20 patients. BCC is discriminated from healthy tissue with 90+/-9% sensitivity and 85+/-9% specificity in a 70% to 30% split cross-validation algorithm. This multivariate model is then applied on tissue sections from new patients to image tumor regions. The RMS images show excellent correlation with the gold standard of histopathology sections, BCC being detected in all positive sections. We demonstrate the potential of RMS as an automated objective method for tumor evaluation during MMS. The replacement of current histopathology during MMS by a ``generalization'' of the proposed technique may improve the feasibility and efficacy of MMS, leading to a wider use according to clinical need.

  18. Cell death stages in single apoptotic and necrotic cells monitored by Raman microspectroscopy

    PubMed Central

    Brauchle, Eva; Thude, Sibylle; Brucker, Sara Y.; Schenke-Layland, Katja

    2014-01-01

    Although apoptosis and necrosis have distinct features, the identification and discrimination of apoptotic and necrotic cell death in vitro is challenging. Immunocytological and biochemical assays represent the current gold standard for monitoring cell death pathways; however, these standard assays are invasive, render large numbers of cells and impede continuous monitoring experiments. In this study, both room temperature (RT)-induced apoptosis and heat-triggered necrosis were analyzed in individual Saos-2 and SW-1353 cells by utilizing Raman microspectroscopy. A targeted analysis of defined cell death modalities, including early and late apoptosis as well as necrosis, was facilitated based on the combination of Raman spectroscopy with fluorescence microscopy. Spectral shifts were identified in the two cell lines that reflect biochemical changes specific for either RT-induced apoptosis or heat-mediated necrosis. A supervised classification model specified apoptotic and necrotic cell death based on single cell Raman spectra. To conclude, Raman spectroscopy allows a non-invasive, continuous monitoring of cell death, which may help shedding new light on complex pathophysiological or drug-induced cell death processes. PMID:24732136

  19. Coexistence of Probe Conformations in Lipid Phases—A Polarized Fluorescence Microspectroscopy Study

    PubMed Central

    Urbančič, Iztok; Ljubetič, Ajasja; Arsov, Zoran; Štrancar, Janez

    2013-01-01

    Several well-established fluorescence methods depend on environment-sensitive probes that report about molecular properties of their local environment. For reliable interpretation of experiments, careful characterization of probes’ behavior is required. In this study, bleaching-corrected polarized fluorescence microspectroscopy with nanometer spectral peak position resolution was applied to characterize conformations of two alkyl chain-labeled 7-nitro-2-1,3-benzoxadiazol-4-yl phospholipids in three model membranes, representing the three main lipid phases. The combination of polarized and spectral detection revealed two main probe conformations with their preferential fluorophore dipole orientations roughly parallel and perpendicular to membrane normal. Their peak positions were separated by 2–6 nm because of different local polarities and depended on lipid environment. The relative populations of conformations, estimated by a numerical model, indicated a specific sensitivity of the two probes to molecular packing with cholesterol. The coexistence of probe conformations could be further exploited to investigate membrane organization below microscopy spatial resolution, such as lipid rafts. With the addition of polarized excitation or detection to any environment-sensitive fluorescence imaging technique, the conformational analysis can be directly applied to explore local membrane complexity. PMID:23972844

  20. Mapping of redox state of mitochondrial cytochromes in live cardiomyocytes using Raman microspectroscopy.

    PubMed

    Brazhe, Nadezda A; Treiman, Marek; Brazhe, Alexey R; Find, Ninett L; Maksimov, Georgy V; Sosnovtseva, Olga V

    2012-01-01

    This paper presents a nonivasive approach to study redox state of reduced cytochromes c, c1 and b of complexes II and III in mitochondria of live cardiomyocytes by means of Raman microspectroscopy. For the first time with the proposed approach we perform studies of rod- and round-shaped cardiomyocytes, representing different morphological and functional states. Raman mapping and cluster analysis reveal that these cardiomyocytes differ in the amounts of reduced cytochromes c, c1 and b. The rod-shaped cardiomyocytes possess uneven distribution of reduced cytochromes c, c1 and b in cell center and periphery. Moreover, by means of Raman spectroscopy we demonstrated the decrease in the relative amounts of reduced cytochromes c, c1 and b in the rod-shaped cardiomyocytes caused by H2O2-induced oxidative stress before any visible changes. Results of Raman mapping and time-dependent study of reduced cytochromes of complexes II and III and cytochrome c in cardiomyocytes are in a good agreement with our fluorescence indicator studies and other published data.

  1. X-ray radiation-induced effects in human mammary epithelial cells investigated by Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Risi, R.; Manti, L.; Perna, G.; Lasalvia, M.; Capozzi, V.; Delfino, I.; Lepore, M.

    2012-06-01

    Micro-Raman technique can be particularly useful to investigate the chemical changes induced in structure, protein, nucleic acid, lipid, and carbohydrate contents of cells. The aim of this work is to inspect the possibility to employ Raman microspectroscopy to detect biochemical modifications in human mammary epithelial cells after exposure to different Xray doses. The samples consisted of cells cultured on polylysine-coated glass coverslips. After the exposition, control and treated cells were washed in phosphate-buffered saline (PBS) and then fixed in paraformaldehyde 3.7%. They were examined using a confocal micro-Raman system equipped with a He-Ne laser (λ = 632.8 nm; power on the sample= 3.5mW). Differences in the intensity ratio of specific Raman vibrational markers commonly assigned to phenylalanine and tyrosine amino acids (at 1000, 1030, 1618 cm-1), DNA bases (787, 1090, 1305 cm-1), and amide III (1237, and 1265 cm-1) with respect a reference peak (the one of lipids at 1450 cm-1) were evidenced between control and exposed cells. These differences may be indicative of damage in exposed cells as the fragmentation of individual amino acids and DNA bases, crosslink effects in molecular structure of DNA and protein conformational change that especially tend to "unwind" the protein due to the breaking of hydrogen bonds between peptide chains.

  2. Characterization of MBa2Cu3O7-x thin films by Raman microspectroscopy.

    PubMed

    Venkataraman, Kartik; Baurceanu, Roxanne; Maroni, Victor A

    2005-05-01

    Thin film embodiments of MBa2Cu3O7-x (MBCO, M = yttrium or a rare-earth metal) prepared by several different deposition methods on a variety of substrates were investigated by Raman microspectroscopy. Several of the unique characterization capabilities of Raman spectroscopy in the analysis of MBCO thin films are highlighted by the results of these investigations. The Raman active phonons of the orthorhombic and tetragonal forms of MBCO that are most useful for characterization of textured MBCO films are diagrammed and discussed. A rapid procedure for qualitative texture mapping of MBCO thin films using Raman microscopy techniques is presented, and a new approach for investigating phase separation at the sub-micrometer level in MBCO thin films based on curve resolution of the MBCO Cu2 phonon is described. The assignment of a particular feature often observed in Raman spectra of MBCO films to cation disorder is reinforced by results of a cation substitution study. The depth of penetration of the laser into MBCO films and the type of information that can be obtained by varying the extent of defocusing of the laser are also discussed.

  3. Vibrational spectroscopy and microspectroscopy analyzing qualitatively and quantitatively pharmaceutical hot melt extrudates.

    PubMed

    Netchacovitch, L; Thiry, J; De Bleye, C; Chavez, P-F; Krier, F; Sacré, P-Y; Evrard, B; Hubert, Ph; Ziemons, E

    2015-09-10

    Since the last decade, more and more Active Pharmaceutical Ingredient (API) candidates have poor water solubility inducing low bioavailability. These molecules belong to the Biopharmaceutical Classification System (BCS) classes II and IV. Thanks to Hot-Melt Extrusion (HME), it is possible to incorporate these candidates in pharmaceutical solid forms. Indeed, HME increases the solubility and the bioavailability of these drugs by encompassing them in a polymeric carrier and by forming solid dispersions. Moreover, in 2004, the FDA's guidance initiative promoted the usefulness of Process Analytical Technology (PAT) tools when developing a manufacturing process. Indeed, the main objective when developing a new pharmaceutical process is the product quality throughout the production chain. The trend is to follow this parameter in real-time in order to react immediately when there is a bias. Vibrational spectroscopic techniques, NIR and Raman, are useful to analyze processes in-line. Moreover, off-line Raman microspectroscopy is more and more used when developing new pharmaceutical processes or when analyzing optimized ones by combining the advantages of Raman spectroscopy and imaging. It is an interesting tool for homogeneity and spatial distribution studies. This review treats about spectroscopic techniques analyzing a HME process, as well off-line as in-line, presenting their advantages and their complementarities. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Cell death stages in single apoptotic and necrotic cells monitored by Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Brauchle, Eva; Thude, Sibylle; Brucker, Sara Y.; Schenke-Layland, Katja

    2014-04-01

    Although apoptosis and necrosis have distinct features, the identification and discrimination of apoptotic and necrotic cell death in vitro is challenging. Immunocytological and biochemical assays represent the current gold standard for monitoring cell death pathways; however, these standard assays are invasive, render large numbers of cells and impede continuous monitoring experiments. In this study, both room temperature (RT)-induced apoptosis and heat-triggered necrosis were analyzed in individual Saos-2 and SW-1353 cells by utilizing Raman microspectroscopy. A targeted analysis of defined cell death modalities, including early and late apoptosis as well as necrosis, was facilitated based on the combination of Raman spectroscopy with fluorescence microscopy. Spectral shifts were identified in the two cell lines that reflect biochemical changes specific for either RT-induced apoptosis or heat-mediated necrosis. A supervised classification model specified apoptotic and necrotic cell death based on single cell Raman spectra. To conclude, Raman spectroscopy allows a non-invasive, continuous monitoring of cell death, which may help shedding new light on complex pathophysiological or drug-induced cell death processes.

  5. NSLS annual report 1984

    SciTech Connect

    Klaffky, R.; Thomlinson, W.

    1984-01-01

    The first comprehensive Annual Report of the National Synchrotron Light Source comes at a time of great activity and forward motion for the facility. In the following pages we outline the management changes that have taken place in the past year, the progress that has been made in the commissioning of the x-ray ring and in the enhanced utilization of the uv ring, together with an extensive discussion of the interesting scientific experiments that have been carried out.

  6. Synchrotron X-ray Tests of an L-Shaped Laterally Graded Multilayer Mirror for the Analyzer System of the Ultra-High Resolution IXS Spectrometer at NSLS-II

    SciTech Connect

    Honnicke, M.G.; Takacs, P.; Keister, J.W.; Conley, R.; Kaznatcheev, K.; Coburn, D.S.; Reffi, L.; Cai, Y.Q.

    2011-08-02

    Characterization and testing of an L-shaped laterally graded multilayer mirror are presented. This mirror is designed as a two-dimensional collimating optics for the analyzer system of the ultra-high-resolution inelastic X-ray scattering (IXS) spectrometer at National Synchrotron Light Source II (NSLS-II). The characterization includes point-to-point reflectivity measurements, lattice parameter determination and mirror metrology (figure, slope error and roughness). The synchrotron X-ray test of the mirror was carried out reversely as a focusing device. The results show that the L-shaped laterally graded multilayer mirror is suitable to be used, with high efficiency, for the analyzer system of the IXS spectrometer at NSLS-II.

  7. Localized (5 μm) probing and detailed mapping of hair with synchrotron powered FT-IR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Wetzel, David L.; Williams, Gwyn P.

    1998-06-01

    The thickness and high absorptivity of single hairs typically result in the saturation of major infrared bands and their distortion. Single human hairs longitudinally microtomed and mounted on mirror slides were scanned routinely in the past with a 20 μm×100 μm aperture that limited spatial resolution for localized probing and detailed mapping. Use of the nondivergent, bright, and low-noise synchrotron source for FT-IR microspectroscopy enables good S/N even at apertures as small as 5-6 μm. Functional group mapping as well as localized probing for extraneous materials illustrates the utility of this powerful probe.

  8. Vibrationally resonant imaging of a single living cell by supercontinuum-based multiplex coherent anti-Stokes Raman scattering microspectroscopy

    NASA Astrophysics Data System (ADS)

    Kano, Hideaki; Hamaguchi, Hiro-O.

    2005-02-01

    Supercontinuum-based multiplex coherent anti-Stokes Raman scattering (CARS) microspectroscopy has been applied to vibrational imaging of a living fission yeast cell. We have successfully extracted only a vibrationally resonant CARS image from a characteristic spectral profile in the C-H stretching vibrational region. Using our simple but sensitive analysis, the vibrational contrast is significantly improved in comparison with a CARS imaging at a fixed Raman shift. The CARS image of a living yeast cell indicates several areas at which the signal is remarkably strong. They are considered to arise from mitochondria.

  9. Measuring Cellular-scale Nutrient Distribution in Algal Biofilms with Synchrotron Confocal Infrared Microspectroscopy

    SciTech Connect

    J Murdock; W Dodds; J Reffner; D Wetzel

    2011-12-31

    The microscope and infrared spectrometer are two of the most useful tools for the study of biological materials, and their combined analytical power far exceeds the sum of the two. Performing molecular spectroscopy through a microscope superimposes chemical information onto the physical microstructure obtained from the optical microscope when visible and infrared information are collected under the same conditions. The instrument developments that enable current infrared microspectroscopic studies began with the introduction of the first research-grade infrared microscope, patented in 1989 (1). By 1993, published reports using this method to determine macroalgae (seaweed) cell-wall composition appeared (2-4). Since these initial reports, the use of infrared microspectroscopy (IMS) in microalgal (single cells or groups of cells) research has grown. Primarily, cultured algae have been used to hone IMS methodology and evaluate its capabilities in algal research (5-8). Studies involving natural, mixed species assemblages, which can utilize the spatial resolution potential of this technique fully are rare (9-11). For instance, in a recent review of IMS microalgal ecological research (12), only 3 of the 29 peer-reviewed publications investigated natural algal assemblages. Both thermal and synchrotron infrared sources provide a resolution capable of measuring individual algae in mixed species assemblages, and each has its advantages. For example, thermal source IMS is more accessible, allowing more samples to be analyzed than synchrotron IMS. However, synchrotron IMS with confocal masking provides superior resolution, which can be critical in isolating small or contiguous cells. Algal ecology is the study of the interaction between algae and their environment. Infrared microspectroscopy addresses a major logistical problem in this field, obtaining species-specific cellular biochemical information from natural, mixed-species assemblages (11,12). Benthic (bottom

  10. Sensitive Skin: Assessment of the Skin Barrier Using Confocal Raman Microspectroscopy.

    PubMed

    Richters, Renée J H; Falcone, Denise; Uzunbajakava, Natallia E; Varghese, Babu; Caspers, Peter J; Puppels, Gerwin J; van Erp, Piet E J; van de Kerkhof, Peter C M

    2017-01-01

    Sensitive skin (SS), a frequently reported condition in the Western world, has been suggested to be underlined by an impaired skin barrier. The aim of this study was to investigate the skin barrier molecular composition in SS subjects using confocal Raman microspectroscopy (CRS), and to compare it with that of non-SS (NSS) individuals as well as atopic dermatitis (AD) and allergic rhinoconjunctivitis (AR) subjects, who frequently report SS. Subjects with SS (n = 29), NSS (n = 30), AD (n = 11), and AR (n = 27) were included. Stratum corneum (SC) thickness, water, ceramides/fatty acids, and natural moisturizing factor (NMF) were measured by CRS along with transepidermal water loss and capacitance on the ventral forearm, thenar, and cheek. Sebum levels were additionally measured on the forearm and cheek. No differences between SS and NSS subjects were found regarding SC thickness, water, and NMF content, yet a trend towards lower ceramides/fatty acids was observed in the cheek. Compared to AD subjects, the SS group showed higher ceramides/fatty acid content in the forearm, whereas no differences emerged with AR. The correlation of macroscopic biophysical techniques and CRS was weak, yet CRS confirmed the well-known lower content of NMF and water, and thinner SC in subjects with filaggrin mutations. The skin barrier in SS is not impaired in terms of SC thickness, water, NMF, and ceramides/fatty acid content. The failure of biophysical techniques to follow alterations in the molecular composition of the skin barrier revealed by CRS emphasizes a strong need in sensitive and specific tools for in vivo skin barrier analysis. © 2017 S. Karger AG, Basel.

  11. Apoptotic pathways of U937 leukemic monocytes investigated by infrared microspectroscopy and flow cytometry.

    PubMed

    Birarda, Giovanni; Bedolla, Diana E; Mitri, Elisa; Pacor, Sabrina; Grenci, Gianluca; Vaccari, Lisa

    2014-06-21

    Apoptosis is a strictly regulated cell death mechanism that plays a pivotal role in the normal evolution of multicellular organisms. Its misregulation has been associated with many diseases, making its early and reliable detection a key point for modern cellular biology. In this paper, we propose the use of infrared microspectroscopy (IRMS) as a label-free methodology for the detection of apoptotic-related biochemical processes induced on U937 leukemic monocytes by serum starvation and CCCP-exposure. The spectroscopic results are in agreement with parallel Flow Cytometry (FC) experiments, where plasma membrane integrity and mitochondrial activity were assessed. Spectroscopic outcomes complement FC data and allow drawing a more complete picture of the apoptotic pathways. In particular, we established that the two apoptosis-inducing treatments, cell starvation and CCCP exposure, affect the cell cycle in a different way. With the former, cell death is preceded by a cell cycle arrest, whereas the latter causes an increased cell cycle progression. Spectral data demonstrate that for both conditions apoptosis proceeds through the accumulation of lipid droplets within cells. Moreover, we were able to establish a spectral marker for DNA condensation/fragmentation: the enhancement of the PhI band component centred at ~1206 cm(-1), which is more sensitive than the relative intensity of the PhII band to which phospholipids and carbohydrates also contribute significantly. In conclusion, we demonstrate that the intrinsic multi-parametric nature of IRMS and its application on cells under physiological conditions can be well exploited for the investigation of apoptotic pathways.

  12. Fourier transform infrared microspectroscopy reveals biochemical changes associated with glioma stem cell differentiation.

    PubMed

    Kenig, Saša; Bedolla, Diana E; Birarda, Giovanni; Faoro, Valentina; Mitri, Elisa; Vindigni, Alessandro; Storici, Paola; Vaccari, Lisa

    2015-12-01

    According to the cancer stem cell theory malignant glioma is incurable because of the presence of the cancer stem cells - a subpopulation of cells that are resistant to therapy and cause the recurrence of a tumor after surgical resection. Several protein markers of cancer stem cell were reported but none of those is fully reliable to grade the content of stem cells in a tumor. Hereby we propose Fourier transform infrared (FTIR) microspectroscopy as an alternative, labelfree, non-damaging and fast method to identify glioma stem cells based on their own spectral characteristics. The analysis of FTIR data revealed that in NCH421k cells, a model of glioma stem cells, the relative content of lipids is higher than in their all-trans retinoic acid-differentiated counterparts. Moreover, it has been assessed that stem cells have more rigid cellular membranes and more phosphorylated proteins, whereas after differentiation glycogen level increases. The ability of FTIR to estimate the content of stem cells in a heterogeneous sample, on the base of the identified spectral markers, and to classify stem and non-stem cells into two separate populations was probed. Although it was not possible to calculate the exact percentage of each subpopulation, we could clearly see that with the increasing amount of differentiated cells in a sample, more hits occupy the PC space previously identified as a space of differentiated cells. The present study is therefore an initial step towards the development of a FTIR based protocol in clinical practice to estimate the content of stem cells in a tumor sample. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. Imaging the Material Properties of Bone Specimens using Reflection-Based Infrared Microspectroscopy

    PubMed Central

    Acerbo, Alvin S.; Carr, G. Lawrence; Judex, Stefan; Miller, Lisa M.

    2012-01-01

    Fourier Transform InfraRed Microspectroscopy (FTIRM) is a widely used method for mapping the material properties of bone and other mineralized tissues, including mineralization, crystallinity, carbonate substitution, and collagen cross-linking. This technique is traditionally performed in a transmission-based geometry, which requires the preparation of plastic-embedded thin sections, limiting its functionality. Here, we theoretically and empirically demonstrate the development of reflection-based FTIRM as an alternative to the widely adopted transmission-based FTIRM, which reduces specimen preparation time and broadens the range of specimens that can be imaged. In this study, mature mouse femurs were plastic-embedded and longitudinal sections were cut at a thickness of 4 μm for transmission-based FTIRM measurements. The remaining bone blocks were polished for specular reflectance-based FTIRM measurements on regions immediately adjacent to the transmission sections. Kramers-Kronig analysis of the reflectance data yielded the dielectric response from which the absorption coefficients were directly determined. The reflectance-derived absorbance was validated empirically using the transmission spectra from the thin sections. The spectral assignments for mineralization, carbonate substitution, and collagen cross-linking were indistinguishable in transmission and reflection geometries, while the stoichiometric/non-stoichiometric apatite crystallinity parameter shifted from 1032 / 1021 cm−1 in transmission-based to 1035 / 1025 cm−1 in reflection-based data. This theoretical demonstration and empirical validation of reflection-based FTIRM eliminates the need for thin sections of bone and more readily facilitates direct correlations with other methods such nanoindentation and quantitative backscatter electron imaging (qBSE) from the same specimen. It provides a unique framework for correlating bone’s material and mechanical properties. PMID:22455306

  14. Fluorescence, aggregation properties and FT-IR microspectroscopy of elastin and collagen fibers.

    PubMed

    Vidal, Benedicto de Campos

    2014-10-01

    Histological and histochemical observations support the hypothesis that collagen fibers can link to elastic fibers. However, the resulting organization of elastin and collagen type complexes and differences between these materials in terms of macromolecular orientation and frequencies of their chemical vibrational groups have not yet been solved. This study aimed to investigate the macromolecular organization of pure elastin, collagen type I and elastin-collagen complexes using polarized light DIC-microscopy. Additionally, differences and similarities between pure elastin and collagen bundles (CB) were investigated by Fourier transform-infrared (FT-IR) microspectroscopy. Although elastin exhibited a faint birefringence, the elastin-collagen complex aggregates formed in solution exhibited a deep birefringence and formation of an ordered-supramolecular complex typical of collagen chiral structure. The FT-IR study revealed elastin and CB peptide NH groups involved in different types of H-bonding. More energy is absorbed in the vibrational transitions corresponding to CH, CH2 and CH3 groups (probably associated with the hydrophobicity demonstrated by 8-anilino-1-naphtalene sulfonic acid sodium salt [ANS] fluorescence), and to νCN, δNH and ωCH2 groups of elastin compared to CB. It is assumed that the α-helix contribution to the pure elastin amide I profile is 46.8%, whereas that of the B-sheet is 20% and that unordered structures contribute to the remaining percentage. An FT-IR profile library reveals that the elastin signature within the 1360-1189cm(-1) spectral range resembles that of Conex-Toray aramid fibers. Copyright © 2014 Elsevier GmbH. All rights reserved.

  15. Topochemistry, optical anisotropy and FT-IR microspectroscopy of the cocoon of Lithurgus chrysurus (Hymenoptera, Megachilidae).

    PubMed

    Mello, Maria Luiza S; Dos Anjos, Eli Heber M; Vidal, Benedicto de Campos; Rozen, Jerome G

    2016-11-01

    A previous study has not revealed the participation of a mucous component in the cocoon wall of the solitary bee, Lithurgus chrysurus, differing from the cocoon structure reported for many other bee species. However, uncertainty remains, because only the median and rear zones of this cocoon type have thus far been analyzed. Here, we studied the front zone of this cocoon, searching its components and their organization, to fill this knowledge gap. Topochemical assays, polarization microscopy and Fourier transform-infrared (FT-IR) microspectroscopy were used to study cross sections from L. chrysurus cocoon. Three main layers differing in structural organization were found to compose the cocoon wall. Silk fibroins were assumed to constitute the filamentous threads of the inner and outer layers and the laminar structure of the intermediate layer. Deduced from its topochemical properties and FT-IR spectral signature, a foamy material containing mucin glycoproteins and carboxylated acid glycosaminoglycans was found in the intermediate layer. FT-IR analysis using a Savitzky-Golay 2nd-derivative and absence of linear dichroism and birefringence phenomena suggest that a random-coil secondary structure predominates in the foam component. Co-existence of α-helical and β-sheet conformations is also hypothesized for the fibroin component of this cocoon. It is thus concluded that in addition to fibroin elements, a mucous component, likely contributed by a Malpighian tubule secretion, integrates the composition of the front zone of the cocoon wall of L. chrysurus. In addition, the FT-IR analysis of the inner layer silk of this cocoon suggests significant differences in comparison to the silk fibroins of the silkworm, and some minor spectral differences in comparison to published data on the honeybee silk, with respect to protein secondary structure. Copyright © 2016 Elsevier Ltd. All rights reserved.

  16. Synchrotron FTIR micro-spectroscopy study of the rat hippocampal formation after pilocarpine-evoked seizures.

    PubMed

    Chwiej, J; Dulinska, J; Janeczko, K; Dumas, P; Eichert, D; Dudala, J; Setkowicz, Z

    2010-10-01

    In the present work, synchrotron radiation Fourier transform infrared (SRFTIR) micro-spectroscopy and imaging were used for topographic and semi-quantitative biochemical analysis of rat brain tissue in cases of pilocarpine-induced epilepsy. The tissue samples were analyzed with a beam defined by small apertures and spatial resolution steps of 10 microm which allowed us to probe the selected cellular layers of hippocampal formation. Raster scanning of the samples has generated 2D chemical cartographies revealing the distribution of proteins, lipids and nucleic acids. Spectral analysis has shown changes in the saturation level of phospholipids and relative secondary structure of proteins. Special interest was put in the analysis of two areas of the hippocampal formation (sector 3 of the Ammon's horn, CA3 and dentate gyrus, DG) in which elemental abnormalities were observed during our previous studies. Statistically significant increase in the saturation level of phospholipids (increased ratio of the absorption intensities at around 2921 and 2958 cm(-1)) as well as conformational changes of proteins (beta-type structure discrepancies as shown by the increased ratio of the absorbance intensities at around 1631 and 1657 cm(-1) as well as the ratio of the absorbance at 1548 and 1657 cm(-1)) were detected in pyramidal cells of CA3 area as well as in the multiform and molecular layers of DG. The findings presented here suggest that abnormalities in the protein secondary structure and increases in the level of phospholipid saturation could be involved in mechanisms of neurodegenerative changes following the oxidative stress evoked in brain areas affected by pilocarpine-induced seizures. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  17. Compositional analysis of metal chelating materials using near-field photothermal Fourier transform infrared microspectroscopy.

    PubMed

    Moffat, Jonathan G; Mayes, Andrew G; Belton, Peter S; Craig, Duncan Q M; Reading, Mike

    2010-01-01

    Photothermal-Fourier transform-infrared (PT-FT-IR) microspectroscopy employs a thermal probe mounted in a scanning probe microscope (SPM). By placement of the tip of the probe on the surface of a solid sample, it can obtain localized IR spectra of a wide range of samples. A second mode of analysis is also available; a sample can be taken from the selected location using a technique called thermally assisted nanosampling (TAN), then a spectrum can be obtained of the nanosample while the probe is remote from the surface. We report a novel method of local compositional analysis that combines both of these types of measurement; a reagent is attached to the tip using TAN, then the reagent is placed in contact with analyte. IR spectroscopy can then be used to analyze any interaction between the reagent and surface it is placed in contact with. All of these modes of analysis were illustrated using a metal chelating agent. In the surface mode, changes to a solid bead of a chelating resin were measured using standard PT-FT-IR. In the nanosampling mode of analysis, a particle of a chelating polymer was attached to the tip of the probe using TAN and this was placed in contact with a concentrated calcium solution. Strong spectral changes were observed that mirrored those found when exposing the surface bound chelating resin bead to a solution of the same ion. A semiquantitative simulation of the PT spectrum for a chelating resin bead was achieved using a thermal diffusion model derived from photoacoustic spectroscopy indicating that semiquantitative or quantitative measurements will be possible in such a system.

  18. The structural analysis of three-dimensional fibrous collagen hydrogels by Raman microspectroscopy.

    PubMed

    Hwang, Yu Jer; Lyubovitsky, Julia G

    2013-06-01

    To investigate molecular effects of 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC), EDC/N-hydroxysuccinimide (NHS), glyceraldehyde cross-linking as well as polymerization temperature and concentration on the three-dimensional (3D) collagen hydrogels, we analyzed the structures in situ by Raman microspectroscopy. The increased intensity of the 814 and 936 cm(-1) Raman bands corresponding to the C-C stretch of a protein backbone and a shift in the amide III bands from 1241 cm(-1)/1268 cm(-1) in controls to 1247 cm(-1)/1283 cm(-1) in glyceraldehyde-treated gels indicated changes to the alignment of the collagen molecules, fibrils/fibers and/or changes to the secondary structure on glyceraldehyde treatment. The increased intensity of 1450 cm(-1) band and the appearance of a strong peak at 1468 cm(-1) reflected a change in the motion of lysine/arginine CH2 groups. For the EDC-treated collagen hydrogels, the increased intensity of 823 cm(-1) peak corresponding to the C-C stretch of the protein backbone indicated that EDC also changed the packing of collagen molecules. The 23% decrease in the ratio of 1238 cm(-1) to 1271 cm(-1) amide III band intensities in the EDC-modified samples compared with the controls indicated changes to the alignment of the collagen molecules/fibrils and/or the secondary structure. A change in the motion of lysine/arginine CH2 groups was detected as well. The addition of NHS did not induce additional Raman shifts compared to the effect of EDC alone with the exception of a 1416 cm(-1) band corresponding to a COO(-) stretch. Overall, the Raman spectra suggest that glyceraldehyde affects the collagen states within 3D hydrogels to a greater extent compared to EDC and the effects of temperature and concentration are minimal and/or not detectable.

  19. Raman microspectroscopy of organic inclusions in spodumenes from Nilaw (Nuristan, Afghanistan).

    PubMed

    Wesełucha-Birczyńska, A; Słowakiewicz, M; Natkaniec-Nowak, L; Proniewicz, L M

    2011-08-15

    The color varieties of spodumene (green spodumene, kunzite) from Nilaw mine (Nuristan, Afghanistan) have been investigated by microthermometry and Raman spectroscopy analyses. These minerals are rich in primary and secondary fluid inclusions. Measured values of temperature homogenization (T(h)) and pressure (P) for selected fluid-inclusion assemblages (I-IV) FIA in green spodumene and (I-II) FIA in kunzite ranges from 370 to 430°C, 1.16 to 1.44 kbar and 300 to 334°C, 0.81 to 1.12 kbar, respectively. The brine content and concentration varies from 4.3 to 6.6 wt.% eq. NaCl. Numerous and diverse mineral phases (quartz, feldspars, mica, beryl, zirconium, apatite, calcite, gypsum) present in this mineral as solid inclusions were studied by Raman microspectroscopy. Raman spectra of selected fluid, organic and solid inclusions were collected as line or rectangular maps and also depth profiles to study their size and contents. There appeared very interesting calcite (156, 283, 711 and 1085 cm(-1)), beryl (324, 397, 686, 1068 and 3610 cm(-1)), topaz (231, 285, 707, 780 and 910 cm(-1)) and spodumene (355, 707 and 1073 cm(-1)) inclusions accompanied by fluid and/or organic inclusions (liquid and gas hydrocarbons) with bands at 2350 cm(-1) (CO(2), N(2)), 2550 cm(-1) (H(2)S) and 2900 cm(-1) (C(2)H(6)-CH(3)). Some solid inclusions contain carbonaceous matter (D-band at ca. 1320 cm(-1) and/or G-band at ca. 1600 cm(-1)).

  20. Sensitive Skin: Assessment of the Skin Barrier Using Confocal Raman Microspectroscopy

    PubMed Central

    Richters, Renée J.H.; Falcone, Denise; Uzunbajakava, Natallia E.; Varghese, Babu; Caspers, Peter J.; Puppels, Gerwin J.; van Erp, Piet E.J.; van de Kerkhof, Peter C.M.

    2017-01-01

    Background/Aims Sensitive skin (SS), a frequently reported condition in the Western world, has been suggested to be underlined by an impaired skin barrier. The aim of this study was to investigate the skin barrier molecular composition in SS subjects using confocal Raman microspectroscopy (CRS), and to compare it with that of non-SS (NSS) individuals as well as atopic dermatitis (AD) and allergic rhinoconjunctivitis (AR) subjects, who frequently report SS. Methods Subjects with SS (n = 29), NSS (n = 30), AD (n = 11), and AR (n = 27) were included. Stratum corneum (SC) thickness, water, ceramides/fatty acids, and natural moisturizing factor (NMF) were measured by CRS along with transepidermal water loss and capacitance on the ventral forearm, thenar, and cheek. Sebum levels were additionally measured on the forearm and cheek. Results No differences between SS and NSS subjects were found regarding SC thickness, water, and NMF content, yet a trend towards lower ceramides/fatty acids was observed in the cheek. Compared to AD subjects, the SS group showed higher ceramides/fatty acid content in the forearm, whereas no differences emerged with AR. The correlation of macroscopic biophysical techniques and CRS was weak, yet CRS confirmed the well-known lower content of NMF and water, and thinner SC in subjects with filaggrin mutations. Conclusion The skin barrier in SS is not impaired in terms of SC thickness, water, NMF, and ceramides/fatty acid content. The failure of biophysical techniques to follow alterations in the molecular composition of the skin barrier revealed by CRS emphasizes a strong need in sensitive and specific tools for in vivo skin barrier analysis. PMID:28122376

  1. Imaging the Material Properties of Bone Specimens Using Reflection-Based Infrared Microspectroscopy

    SciTech Connect

    Acerbo A. S.; Carr, G.L.; Judex, S.; Miller, L.M.

    2012-03-13

    Fourier transform infrared microspectroscopy (FTIRM) is a widely used method for mapping the material properties of bone and other mineralized tissues, including mineralization, crystallinity, carbonate substitution, and collagen cross-linking. This technique is traditionally performed in a transmission-based geometry, which requires the preparation of plastic-embedded thin sections, limiting its functionality. Here, we theoretically and empirically demonstrate the development of reflection-based FTIRM as an alternative to the widely adopted transmission-based FTIRM, which reduces specimen preparation time and broadens the range of specimens that can be imaged. In this study, mature mouse femurs were plastic-embedded and longitudinal sections were cut at a thickness of 4 {micro}m for transmission-based FTIRM measurements. The remaining bone blocks were polished for specular reflectance-based FTIRM measurements on regions immediately adjacent to the transmission sections. Kramers-Kronig analysis of the reflectance data yielded the dielectric response from which the absorption coefficients were directly determined. The reflectance-derived absorbance was validated empirically using the transmission spectra from the thin sections. The spectral assignments for mineralization, carbonate substitution, and collagen cross-linking were indistinguishable in transmission and reflection geometries, while the stoichiometric/nonstoichiometric apatite crystallinity parameter shifted from 1032/1021 cm{sup -1} in transmission-based to 1035/1025 cm{sup -1} in reflection-based data. This theoretical demonstration and empirical validation of reflection-based FTIRM eliminates the need for thin sections of bone and more readily facilitates direct correlations with other methods such as nanoindentation and quantitative backscatter electron imaging (qBSE) from the same specimen. It provides a unique framework for correlating bone's material and mechanical properties.

  2. Raman microspectroscopy of organic inclusions in spodumenes from Nilaw (Nuristan, Afghanistan)

    NASA Astrophysics Data System (ADS)

    Wesełucha-Birczyńska, A.; Słowakiewicz, M.; Natkaniec-Nowak, L.; Proniewicz, L. M.

    2011-08-01

    The color varieties of spodumene (green spodumene, kunzite) from Nilaw mine (Nuristan, Afghanistan) have been investigated by microthermometry and Raman spectroscopy analyses. These minerals are rich in primary and secondary fluid inclusions. Measured values of temperature homogenization ( Th) and pressure ( P) for selected fluid-inclusion assemblages (I-IV) FIA in green spodumene and (I-II) FIA in kunzite ranges from 370 to 430 °C, 1.16 to 1.44 kbar and 300 to 334 °C, 0.81 to 1.12 kbar, respectively. The brine content and concentration varies from 4.3 to 6.6 wt.% eq. NaCl. Numerous and diverse mineral phases (quartz, feldspars, mica, beryl, zirconium, apatite, calcite, gypsum) present in this mineral as solid inclusions were studied by Raman microspectroscopy. Raman spectra of selected fluid, organic and solid inclusions were collected as line or rectangular maps and also depth profiles to study their size and contents. There appeared very interesting calcite (156, 283, 711and 1085 cm -1), beryl (324, 397, 686, 1068 and 3610 cm -1), topaz (231, 285, 707, 780 and 910 cm -1) and spodumene (355, 707 and 1073 cm -1) inclusions accompanied by fluid and/or organic inclusions (liquid and gas hydrocarbons) with bands at 2350 cm -1 (CO 2, N 2), 2550 cm -1 (H 2S) and 2900 cm -1 (C 2H 6-CH 3). Some solid inclusions contain carbonaceous matter (D-band at ca. 1320 cm -1 and/or G-band at ca. 1600 cm -1).

  3. Evaluation of the suitability of ex vivo handled ovarian tissues for optical diagnosis by Raman microspectroscopy.

    PubMed

    Krishna, C Murali; Sockalingum, G D; Venteo, L; Bhat, Rani A; Kushtagi, Pralhad; Pluot, M; Manfait, M

    2005-12-05

    A pilot Raman microspectroscopy study of formalin-fixed, paraffin-embedded, and deparaffinized sections from the same ovarian normal and malignant tissues was carried out. This approach was considered in order to evaluate the suitability of these ex vivo tissue handling procedures in discrimination as well as biochemical characterization. The spectra of formalin-fixed normal and malignant tissues exhibited no contamination due to formalin, which is indicated by the absence of strong formalin peaks; spectral features also show significant differences for normal and malignant tissues. The differences between spectral profiles of deparaffinized normal and malignant tissues are subtle and spectra show few residual sharp peaks of paraffin. Complete dominance of paraffin swamping signals from tissues was observed in the spectra of paraffin-embedded tissues. Principal components analysis (PCA), which was employed for discrimination of tissue type, provided good discrimination for formalin-fixed and paraffin-embedded tissue spectra. PCA of deparaffinized tissues resulted in a poor classification with significant overlap among the clusters. Thus, this study indicates that formalin fixation is the most suitable among the three procedures employed in the study. Significant differences between spectral profiles of normal and malignant formalin-fixed tissues can not only be exploited for discrimination but can also provide information on biochemical characteristics of the tissues. Deparaffinized tissues provide poor discrimination and information on tissue biochemistry is lost. Paraffin-embedded tissues may provide good discrimination, but predominance of paraffin in the spectra could jeopardize biochemical characterization. Prospectively, as a result of the better availability of paraffin-embedded tissues and problems associated with frozen sectioning of formalin-fixed tissues, the results of this study using paraffin-embedded tissues are very encouraging.

  4. Infared Spectroscopy of Discrete Uranyl Anion Complexes

    SciTech Connect

    Groenewold, G. S.; Gianotto, Anita K.; McIIwain, Michael E.; Van Stipdonk, Michael J.; Kullman, Michael; Moore, David T.; Polfer, Nick; Oomens, Jos; Infante, Ivan A.; Visscher, Lucas; Siboulet, Bertrand; De Jong, Wibe A.

    2008-01-24

    The Free-Electron Laser for Infrared Experiments (FELIX) w 1 as used to study the wavelength-resolved multiple photon photodissociation of discrete, gas phase uranyl (UO2 2 2+) complexes containing a single anionic ligand (A), with or without ligated solvent molecules (S). The uranyl antisymmetric and symmetric stretching frequencies were measured for complexes with general formula [UO2A(S)n]+, where A was either hydroxide, methoxide, or acetate; S was water, ammonia, acetone, or acetonitrile; and n = 0-3. The values for the antisymmetric stretching frequency for uranyl ligated with only an anion ([UO2A]+) were as low or lower than measurements for [UO2]2+ ligated with as many as five strong neutral donor ligands, and are comparable to solution phase values. This result was surprising because initial DFT calculations predicted values that were 30–40 cm-1 higher, consistent with intuition but not with the data. Modification of the basis sets and use of alternative functionals improved computational accuracy for the methoxide and acetate complexes, but calculated values for the hydroxide were greater than the measurement regardless of the computational method used. Attachment of a neutral donor ligand S to [UO2A]+ produced [UO2AS]+, which produced only very modest changes to the uranyl antisymmetric stretch frequency, and did not universally shift the frequency to lower values. DFT calculations for [UO2AS]+ were in accord with trends in the data, and showed that attachment of the solvent was accommodated by weakening of the U-anion bond as well as the uranyl. When uranyl frequencies were compared for [UO2AS]+ species having different solvent neutrals, values decreased with increasing neutral nucleophilicity.

  5. Hidden quasars in ultraluminous infared galaxies

    SciTech Connect

    Brotherton, M S; Stanford, S A; Tran, H; van Breugel, W

    1998-08-27

    Abstract. Many ultraluminous infrared galaxies (ULIRGS) are pow- ered by quasars hidden in the center, but many are also powered by starbursts. A simply diagnostic diagram is proposed that can iden- tify obscured quasars in ULIRGs by their high-ionization emission lines ([O III]λ5007/Hβ ≳ 5), and "warm" IR color (ƒ2560 ≳ 0.25).

  6. Label-free nonenzymatic glycation monitoring of collagen scaffolds in type 2 diabetic mice by confocal Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Shi, Panpan; Liu, Hanping; Deng, Xiaoyuan; Jin, Ying; Wang, Qiannan; Liu, Hao; Chen, Maosheng; Han, Xue

    2015-02-01

    Collagen is the key target of nonenzymatic glycation during physiopathological processes such as diabetes. The induced changes in the biochemical property of collagen by nonenzymatic glycation remain a major challenge to probe. This study investigated the use of confocal Raman microspectroscopy to label-free monitor the nonenzymatic glycation of collagen scaffolds from type 2 diabetic (T2D) mice at different timepoints (0, 4, 8, and 12 weeks). The glycated collagen scaffolds were obtained through the decellularized dermal matrix method to remove the epidermis layer, subcutaneous tissue, and cells in the dermis and to retain the collagen fibrils. Raman spectra showed no changes in Raman peak positions, which indicated that nonenzymatic glycation could produce no significant changes in the triple-helix structure of collagen in T2D mice. However, the relative intensity of the Raman bands at 921, 1033, 1244, 1274, 1346, 1635, and 1672 cm-1 increased as diabetic time progressed. Correlation analysis suggested that the spectra of these bands had a high positive correlation with the expression of anti-advanced glycation end products obtained by immunofluorescence imaging of the same collagen scaffolds. Confocal Raman microspectroscopy proves a potential tool to label-free monitor the collagen changes caused by nonenzymatic glycation in T2D mice.

  7. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

    DOE PAGES

    Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja; ...

    2015-08-31

    The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries andmore » microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). Lastly, the described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.« less

  8. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

    SciTech Connect

    Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja; Schintlmeister, Arno; Wagner, Michael; Woebken, Dagmar; Haggblom, Max

    2015-08-31

    The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). Lastly, the described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing.

  9. Process Analytical Utility of Raman Microspectroscopy in the Directed Differentiation of Human Pancreatic Insulin-Positive Cells.

    PubMed

    Konorov, Stanislav O; Schulze, H Georg; Gage, Blair K; Kieffer, Timothy J; Piret, James M; Blades, Michael W; Turner, Robin F B

    2015-11-03

    Continued advances toward cell-based therapies for human disease generate a growing need for unbiased and label-free monitoring of cellular characteristics. We used Raman microspectroscopy to characterize four important stages in the 26-day directed differentiation of human embryonic stem cells (hESCs) to insulin-positive cells. The extent to which the cells retained spectroscopic features of pluripotent cells or developed spectroscopic features suggestive of pancreatic endocrine cells, as well as assessing the homogeneity of the cell populations at these developmental stages, were of particular interest. Such information could have implications for the utility of Raman microspectroscopy process analysis for the generation of insulin-positive cells from hESCs. Because hESC seeding density influences the subsequent pancreatic development, three different seeding density cultures were analyzed. Transcription factor and other marker analyses assessed the progress of the cells through the relevant developmental stages. Increases in the Raman protein-to-nucleic acid band ratios were observed at the final endocrine stage analyzed, but this increase was less than expected. Also, high glycogen band intensities, somewhat unexpected in pancreatic endocrine cells, suggested the presence of a substantial number of glycogen containing cells. We discuss the potential process analytical technology application of these findings and their importance for cell manufacturing.

  10. In situ characterization of protein aggregates in human tissues affected by light chain amyloidosis: a FTIR microspectroscopy study

    PubMed Central

    Ami, Diletta; Lavatelli, Francesca; Rognoni, Paola; Palladini, Giovanni; Raimondi, Sara; Giorgetti, Sofia; Monti, Luca; Doglia, Silvia Maria; Natalello, Antonino; Merlini, Giampaolo

    2016-01-01

    Light chain (AL) amyloidosis, caused by deposition of amyloidogenic immunoglobulin light chains (LCs), is the most common systemic form in industrialized countries. Still open questions, and premises for developing targeted therapies, concern the mechanisms of amyloid formation in vivo and the bases of organ targeting and dysfunction. Investigating amyloid material in its natural environment is crucial to obtain new insights on the molecular features of fibrillar deposits at individual level. To this aim, we used Fourier transform infrared (FTIR) microspectroscopy for studying in situ unfixed tissues (heart and subcutaneous abdominal fat) from patients affected by AL amyloidosis. We compared the infrared response of affected tissues with that of ex vivo and in vitro fibrils obtained from the pathogenic LC derived from one patient, as well as with that of non amyloid-affected tissues. We demonstrated that the IR marker band of intermolecular β-sheets, typical of protein aggregates, can be detected in situ in LC amyloid-affected tissues, and that FTIR microspectroscopy allows exploring the inter- and intra-sample heterogeneity. We extended the infrared analysis to the characterization of other biomolecules embedded within the amyloid deposits, finding an IR pattern that discloses a possible role of lipids, collagen and glycosaminoglycans in amyloid deposition in vivo. PMID:27373200

  11. Time-resolved FT-IR microspectroscopy of protein aggregation induced by heat-shock in live cells.

    PubMed

    Mitri, Elisa; Kenig, Saša; Coceano, Giovanna; Bedolla, Diana E; Tormen, Massimo; Grenci, Gianluca; Vaccari, Lisa

    2015-04-07

    Maintaining the correct folding of cellular proteins is essential for preserving cellular homeostasis. Protein dishomeostasis, aberrant protein folding, and protein aggregation are indeed involved in several diseases including cancer, aging-associated, and neurodegenerative disorders. Accumulation of protein aggregates can also be induced from a variety of stressful conditions, such as temperature increase or oxidative stress. In this work, we monitored by Fourier transform-infrared (FT-IR) microspectroscopy the response of live breast cancer MCF-7 and mammary breast adenocarcinoma MDA-MB 231 cell lines to severe heat-shock (HS), caused by the rise of the cellular medium temperature from 37 ± 0.5 °C to 42 ± 0.5 °C. Through the study of the time-evolution of the second derivatives of the spectra and by the 2D correlation analysis of FT-IR absorbance data, we were able to identify a common sudden heat-shock response (HSR) among the two cell lines. The hyperfluidization of mammalian cell membranes, the transient increment of the signal lipids, as well as the alteration of proteome profile were all monitored within the first 40 min of stress application, while the persistent intracellular accumulation of extended β-folded protein aggregates was detected after 40 min up to 2 h. As a whole, this paper offers a further prove of the diagnostic capabilities of FT-IR microspectroscopy for monitoring in real-time the biochemical rearrangements undergone by live cells upon external stimulation.

  12. Tracking the cell hierarchy in the human intestine using biochemical signatures derived by mid-infrared microspectroscopy.

    PubMed

    Walsh, Michael J; Hammiche, Azzedine; Fellous, Tariq G; Nicholson, James M; Cotte, Marine; Susini, Jean; Fullwood, Nigel J; Martin-Hirsch, Pierre L; Alison, Malcolm R; Martin, Francis L

    2009-07-01

    Markers of gastrointestinal (GI) stem cells remain elusive. We employed synchrotron Fourier-transform infrared (FTIR) microspectroscopy to derive mid-infrared (IR) spectra along the length of human GI crypts. Tissue sections (10-μm thick) were floated onto BaF2 windows and image maps were acquired of small intestine and large bowel crypts in transmission mode with an aperture of ≤10 μm×10 μm. Counting upwards in a step-size (≤10 μm) fashion from the crypt base, IR spectra were extracted from the image maps and each spectrum corresponding to a particular location was identified. Spectra were analyzed using principal component analysis plus linear discriminant analysis. Compared to putative crypt base columnar/Paneth cells, those assigned as label-retaining cells were chemically more similar to putative large bowel stem cells and, the small intestine transit-amplifying cells were closest to large bowel transit-amplifying cells; interestingly, the base of small intestine crypts was the most chemically-distinct. This study suggests that in the complex cell lineage of human GI crypts, chemical similarities as revealed by FTIR microspectroscopy between regions putatively assigned as stem cell, transit-amplifying and terminally-differentiated facilitates identification of cell function.

  13. Infrared microspectroscopy detects protein misfolding cyclic amplification (PMCA)-induced conformational alterations in hamster scrapie progeny seeds.

    PubMed

    Daus, Martin L; Wagenführ, Katja; Thomzig, Achim; Boerner, Susann; Hermann, Peter; Hermelink, Antje; Beekes, Michael; Lasch, Peter

    2013-12-06

    The self-replicative conformation of misfolded prion proteins (PrP) is considered a major determinant for the seeding activity, infectiousness, and strain characteristics of prions in different host species. Prion-associated seeding activity, which converts cellular prion protein (PrP(C)) into Proteinase K-resistant, infectious PrP particles (PrP(TSE)), can be monitored in vitro by protein misfolding cyclic amplification (PMCA). Thus, PMCA has been established as a valuable analytical tool in prion research. Currently, however, it is under discussion whether prion strain characteristics are preserved during PMCA when parent seeds are amplified in PrP(C) substrate from the identical host species. Here, we report on the comparative structural analysis of parent and progeny (PMCA-derived) PrP seeds by an improved approach of sensitive infrared microspectroscopy. Infrared microspectroscopy revealed that PMCA of native hamster 263K scrapie seeds in hamster PrP(C) substrate caused conformational alterations in progeny seeds that were accompanied by an altered resistance to Proteinase K, higher sedimentation velocities in gradient ultracentrifugations, and a longer incubation time in animal bioassays. When these progeny seeds were propagated in hamsters, misfolded PrP from brain extracts of these animals showed mixed spectroscopic and biochemical properties from both parental and progeny seeds. Thus, strain modifications of 263K prions induced by PMCA seem to have been partially reversed when PMCA products were reinoculated into the original host species.

  14. The influence of high fat diets with different ketogenic ratios on the hippocampal accumulation of creatine - FTIR microspectroscopy study

    NASA Astrophysics Data System (ADS)

    Skoczen, A.; Setkowicz, Z.; Janeczko, K.; Sandt, Ch.; Borondics, F.; Chwiej, J.

    2017-09-01

    The main purpose of this study was the determination and comparison of anomalies in creatine (Cr) accumulation occurring within CA3 and DG areas of hippocampal formation as a result of two high-fat, carbohydrate-restricted ketogenic diets (KD) with different ketogenic ratio (KR). To reach this goal, Fourier transformed infrared microspectroscopy with synchrotron radiation source (SRFTIR microspectroscopy) was applied for chemical mapping of creatine absorption bands, occurring around 1304, 1398 and 2800 cm- 1. The samples were taken from three groups of experimental animals: control group (N) fed with standard laboratory diet, KD1 and KD2 groups fed with high-fat diets with KR 5:1 and 9:1 respectively. Additionally, the possible influence on the phosphocreatine (PhCr, the high energetic form of creatine) content was evaluated by comparative analysis of chemical maps obtained for creatine and for compounds containing phosphate groups which manifest in the spectra at the wavenumbers of around 1240 and 1080 cm- 1. Our results showed that KD2 strongly modifies the frequency of Cr inclusions in both analyzed hippocampal areas. Statistical analysis, performed with Mann-Whitney U test revealed increased accumulation of Cr within CA3 and DG areas of KD2 fed rats compared to both normal rats and KD1 experimental group. Moreover, KD2 diet may modify the frequency of PhCr deposits as well as the PhCr to Cr ratio.

  15. Advancements in the application of NanoSIMS and Raman microspectroscopy to investigate the activity of microbial cells in soils

    PubMed Central

    Eichorst, Stephanie A.; Strasser, Florian; Woyke, Tanja; Schintlmeister, Arno; Wagner, Michael; Woebken, Dagmar

    2015-01-01

    The combined approach of incubating environmental samples with stable isotope-labeled substrates followed by single-cell analyses through high-resolution secondary ion mass spectrometry (NanoSIMS) or Raman microspectroscopy provides insights into the in situ function of microorganisms. This approach has found limited application in soils presumably due to the dispersal of microbial cells in a large background of particles. We developed a pipeline for the efficient preparation of cell extracts from soils for subsequent single-cell methods by combining cell detachment with separation of cells and soil particles followed by cell concentration. The procedure was evaluated by examining its influence on cell recoveries and microbial community composition across two soils. This approach generated a cell fraction with considerably reduced soil particle load and of sufficient small size to allow single-cell analysis by NanoSIMS, as shown when detecting active N2-fixing and cellulose-responsive microorganisms via 15N2 and 13C-UL-cellulose incubations, respectively. The same procedure was also applicable for Raman microspectroscopic analyses of soil microorganisms, assessed via microcosm incubations with a 13C-labeled carbon source and deuterium oxide (D2O, a general activity marker). The described sample preparation procedure enables single-cell analysis of soil microorganisms using NanoSIMS and Raman microspectroscopy, but should also facilitate single-cell sorting and sequencing. PMID:26324854

  16. Casting new physicochemical light on the fundamental biological processes in single living cells by using Raman microspectroscopy.

    PubMed

    Kaliaperumal, Venkatesh; Hamaguchi, Hiro-o

    2012-12-01

    This Personal Account highlights the capabilities of spontaneous Raman microspectroscopy for studying fundamental biological processes in a single living cell. Raman microspectroscopy provides time- and space-resolved vibrational Raman spectra that contain detailed information on the structure and dynamics of biomolecules in a cell. By using yeast as a model system, we have made great progress in the development of this methodology. The results that we have obtained so far are described herein with an emphasis placed on how three cellular processes, that is, cell-division, respiration, and cell-death, are traced and elucidated with the use of time- and space-resolved structural information that is extracted from the Raman spectra. For cell-division, compositional- and structural changes of various biomolecules are observed during the course of the whole cell cycle. For respiration, the redox state of mitochondrial cytochromes, which is inferred from the resonance Raman bands of cytochromes, is used to evaluate the respiration activity of a single cell, as well as that of isolated mitochondrial particles. Special reference is made to the "Raman spectroscopic signature of life", which is a characteristic Raman band at 1602 cm(-1) that is found in yeast cells. This signature reflects the cellular metabolic activity and may serve as a measure of mitochondrial dysfunction. For cell-death, "cross-talk" between the mitochondria and the vacuole in a dying cell is suggested. Copyright © 2012 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

  17. Label-free nonenzymatic glycation monitoring of collagen scaffolds in type 2 diabetic mice by confocal Raman microspectroscopy.

    PubMed

    Shi, Panpan; Liu, Hanping; Deng, Xiaoyuan; Jin, Ying; Wang, Qiannan; Liu, Hao; Chen, Maosheng; Han, Xue

    2015-02-01

    Collagen is the key target of nonenzymatic glycation during physiopathological processes such as diabetes. The induced changes in the biochemical property of collagen by nonenzymatic glycation remain a major challenge to probe. This study investigated the use of confocal Raman microspectroscopy to labelfree monitor the nonenzymatic glycation of collagen scaffolds from type 2 diabetic (T2D) mice at different timepoints (0, 4, 8, and 12 weeks). The glycated collagen scaffolds were obtained through the decellularized dermal matrix method to remove the epidermis layer, subcutaneous tissue, and cells in the dermis and to retain the collagen fibrils. Raman spectra showed no changes in Raman peak positions, which indicated that nonenzymatic glycation could produce no significant changes in the triple-helix structure of collagen in T2D mice. However, the relative intensity of the Raman bands at 921, 1033, 1244, 1274, 1346, 1635, and 1672 cm−1 increased as diabetic time progressed. Correlation analysis suggested that the spectra of these bands had a high positive correlation with the expression of anti-advanced glycation end products obtained by immunofluorescence imaging of the same collagen scaffolds. Confocal Raman microspectroscopy proves a potential tool to label-free monitor the collagen changes caused by nonenzymatic glycation in T2D mice. © 2015 Society of Photo-Optical Instrumentation Engineers (SPIE)

  18. Fourier transform infrared microspectroscopy reveals that tissue culture conditions affect the macromolecular phenotype of human embryonic stem cells.

    PubMed

    Cao, Julie; Ng, Elizabeth S; McNaughton, Don; Stanley, Edouard G; Elefanty, Andrew G; Tobin, Mark J; Heraud, Philip

    2013-07-21

    We employed Fourier transform infrared (FTIR) microspectroscopy to investigate the effects of different tissue culture environments on the FTIR spectra of undifferentiated human embryonic stem cells (hESCs) and their differentiated progeny. First we tested whether there were any possible spectral artifacts resulting from the use of transflectance measurements by comparing them with transmission measurements and found no evidence of these concluding that the lack of any differences resulted from the homogeneity of the dried cytospun cellular monolayers. We found that hESCs that were enzymatically passaged onto mouse embryonic fibroblasts (MEFs) in KOSR based hESC medium, hESCs enzymatically passaged onto Matrigel in mTESR medium and hESCs mechanically passaged onto MEFs in KOSR-based hESC medium, possessed unique FTIR spectroscopic signatures that reflect differences in their macromolecular chemistry. Further, these spectroscopic differences persisted even upon differentiation towards mesendodermal lineages. Our results suggest that FTIR microspectroscopy is a powerful, objective, measurement modality that complements existing methods for studying the phenotype of hESCs and their progeny, particularly changes induced by the cellular environment.

  19. Discrimination of micromass-induced chondrocytes from human mesenchymal stem cells by focal plane array-Fourier transform infrared microspectroscopy.

    PubMed

    Chonanant, Chirapond; Bambery, Keith R; Jearanaikoon, Nichada; Chio-Srichan, Sirinart; Limpaiboon, Temduang; Tobin, Mark J; Heraud, Philip; Jearanaikoon, Patcharee

    2014-12-01

    Rapid and sensitive methods for identifying stem cell differentiation state are required for facilitating future stem cell therapies. We aimed to evaluate the capability of focal plane array-Fourier transform infrared (FPA-FTIR) microspectroscopy for characterising the differentiation of chondrocytes from human mesenchymal stem cells (hMSCs). Successful induction was validated by reverse transcription polymerase chain reaction (RT-PCR) and Western blot analysis for collagen and aggrecan expression as chondrocyte markers in parallel with the spectroscopy. Spectra derived from chondrocyte-induced cells revealed strong IR absorbance bands attributed to collagen near 1338 and 1234 cm(-1) and proteoglycan at 1245 and 1175-960 cm(-1) compared to the non-induced cells. In addition, spectra from control and induced cells are segregated into separate clusters in partial least squares discriminant analysis score plots at the very early stages of induction and discrimination of an independent set of validation spectra with 100% accuracy. The predominant bands responsible for this discrimination were associated with collagen and aggrecan protein concordant with those obtained from RT-PCR and Western blot techniques. Our findings support the capability of FPA-FTIR microspectroscopy as a label-free tool for stem cell characterization allowing rapid and sensitive detection of macromolecular changes during chondrogenic differentiation. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. A study of the single SGC7901 and GES1 cell using synchrotron infrared microspectroscopy and imaging

    NASA Astrophysics Data System (ADS)

    Wang, Xin; Qi, Zeming; Wang, Shengyi; Hu, Meicong; Liu, Gang; Tian, Yangchao

    2011-05-01

    In order to obtain unique information of the single gastric cancer cell and investigate gastric cancer further at the cellular and subcellular level, synchrotron infrared (SR-IR) microspectroscopy and imaging was used to study human gastric adenocarcinoma cell line SGC7901 and normal gastric mucosal epithelial cell line GES1. When we compared the infrared micro-spectra of the SGC7901 cells with those of the GES1 cells, the peak height ratios of 1121 cm -1/1020 cm -1 (RNA/DNA) of the SGC7901 cells were significantly higher than those of the GES1 cells, which might be useful for distinguishing malignant cells from normal cells. Furthermore, chemical imaging reveals that the amide II/the amide I ratio of the SGC7901 cell is lower than that of the GES1 cell in the most intense absorption region of vPO2-. The result indicates the study of the single gastric cancer cell at subcellular level by synchrotron infrared microspectroscopy and imaging can provide more detailed information which is very helpful for the research and diagnosis of gastric cancer.

  1. Application of synchrotron FTIR microspectroscopy for determination of spatial distribution of methylene blue conjugated onto a SAM via"click" chemistry.

    PubMed

    Cañete, Socrates Jose P; Zhang, Zhengzheng; Kong, Lingmei; Schlegel, Vicki L; Plantz, Bradley A; Dowben, Peter A; Lai, Rebecca Y

    2011-11-21

    We report, for the first time, the application of synchrotron FTIR microspectroscopy to determine the spatial distribution of methylene blue conjugated onto a self-assembled monolayer surface via Sharpless "click" chemistry. This journal is © The Royal Society of Chemistry 2011

  2. The investigation of chemical structure of coal macerals via transmitted-light FT-IR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Xuguang, Sun

    2005-11-01

    The Late Permian coals from South China are characterized by high content of the unique maceral "barkinite" and elemental hydrogen, typically produce high yields of tar, and exhibit significant oil-producing potential. "Barkinite" has been identified as suberinite for a long time, but now many Chinese workers have concluded that "barkinite" is not suberinite, rather it is a distinct maceral. The term "barkinite" was formally certified and named by the State Bureau of Technical Supervision of PR China in 1991, 1995, and 1999, however, it has not been recognized as a scientific term by international coal geologists and the ICCP. Transmitted-light FT-IR microspectroscopy and curve-fitting analysis were used to investigate the chemical structure of "barkinite"; at the same time, parallel studies were also carried out on vitrinite, fusinite, and sporinite. In comparison with other maceral types, the micro-FT-IR spectra of "barkinite" are characterized by very strong intensities of aliphatic CH x stretching vibrations at 3000-2800 cm -1 and deformations at 1460-1450 cm -1, less intense bands from aromatic C dbnd C ring stretching at 1610-1600 cm -1 and aromatic CH out-of-plane deformations at 900-700 cm -1. The aliphatic side-chains in the molecular structure of "barkinite" are longer and less branched. In addition, there also appear intense aliphatic ether C sbnd O sbnd C and alcohol C sbnd O stretching bands at 1100-1000 cm -1, notable aromatic CH stretching vibrations at 3050-3030 cm -1, weak OH stretching bands of water in the 3600-3200 cm -1 range, and rare acid C dbnd O group absorption at 1740-1700 cm -1. Collectively the IR spectral characteristics indicate that "barkinite" is composed of great numbers of long chain aliphatics, a fewer of aromatics and rare of oxygenate components. The chemical structure of "barkinite" show that the high tar yields and the relatively high oil-producing potential of the Late Permian coals from South China are attributable to the

  3. Background research in support of the new grant proposal: research consortium for x-ray topography on line X-19 at NSLS

    SciTech Connect

    Bilello, J.C.

    1983-11-01

    The basic design phase of the Synchrotron Topographic Project has been completed and a description of this work has been reported by Bilello et al. Construction of several major components of the Synchrotron Topography Station (STS) has already been completed and installed at the facility. The experimental hutch, control room, and portable darkroom chamber have been completed. Assembly of the computer hardware components, including a PDP 11/23, printer, mag-tape down loader/backup system and motor controller assembly has been completed. Work is continuing on hardware for interfacing, and on software development for interactively controlling, the 13 motors which will automate the experimental facility. The White Beam Camera, film-plate dispenser, Real-time TV alignment camera, and motorized lift table assembly are completed. These components are shown as -installed at STS. Finally a number of other major pieces of apparatus are finished, but await completion of services (electric power, water, drains etc.) to the hutch and suitable operation of the x-ray ring to make alignment possible, before installation at NSLS. Research work has focussed on problems of x-ray optics and on developing new techniques for applying topography to problems in materials science.

  4. Cryogenic Field Measurement of Pr{sub 2}Fe{sub 14}B Undulator and Performance Enhancement Options at the NSLS-II

    SciTech Connect

    Tanabe, Toshiya; Chubar, Oleg; Harder, David A.; Rank, James; Spataro, Charles; Lehecka, Michael; Rakowsky, George

    2010-06-23

    Short period (14.5mm) hybrid undulator arrays composed of Praseodymium Iron Boron (Pr{sub 2}Fe{sub 14}B) magnets (CR53, NEOMAX, Inc.) and vanadium permendur poles have been fabricated at Brookhaven National Laboratory. Unlike Neodymium Iron Boron (Nd{sub 2}Fe{sub 14}B) magnets which exhibit spin reorientation at a temperatures below 150 K, PrFeB arrays monotonically increase performance with lower operating temperature. It opens up the possibility for use in operating a cryo-permanent magnet undulator (CPMU) in the range of 40 K to 60 K where very efficient cryocoolers are available. Magnetic flux density profiles were measured at various temperature ranges from room temperature down to liquid helium (LHe) using the Vertical Testing Facility (VTF) at the National Synchrotron Light Source-II (NSLS-II). Temperature variations of phase error have been characterized. In addition, we examined the use of textured Dysprosium (Dy) poles to replace permendur poles to obtain further improvement in performance.

  5. Synchrotron-based Infrared-microspectroscopy reveals the impact of land management on carbon storage in soil micro-aggregates

    NASA Astrophysics Data System (ADS)

    Hernandez-Soriano, Maria C.; Dalal, Ram C.; Menzies, Neal W.; Kopittke, Peter M.

    2015-04-01

    Carbon stabilization in soil microaggregates results from chemical and biological processes that are highly sensitive to changes in land use. Indeed, such processes govern soil capability to store carbon, this being essential for soil health and productivity and to regulate emissions of soil organic carbon (SOC) as CO2. The identification of carbon functionalities using traditional mid-infrared analysis can be linked to carbon metabolism in soil but differences associated to land use are generally limited. The spatial resolution of synchrotron-based Infrared-microspectroscopy allows mapping microaggregate-associated forms of SOC because it has 1000 times higher brightness than a conventional thermal globar source. These maps can contribute to better understand molecular organization of SOC, physical protection in the soil particles and co-localization of carbon sources with microbial processes. Spatially-resolved analyses of carbon distribution in micro-aggregates (<200 μm diameter) have been conducted using FTIR microspectroscopy (Infrared Microspectroscopy beamline, Australian Synchrotron). Two soil types (Ferralsol and Vertisol, World Reference Base 2014) were collected from undisturbed areas and from a location(s) immediately adjacent which has a long history of agricultural use (>20 years). Soils were gently screened (250 μm) to obtain intact microaggregates which were humidified and frozen at -20°C, and sectioned (200 μm thickness) using a diamond knife and a cryo-ultramicrotome. The sections were placed between CaF2 windows and the spectra were acquired in transmission mode. The maps obtained (5 µm step-size over ca. 150 × 150 µm) revealed carbon distribution in microaggregates from soils under contrasting land management, namely undisturbed and cropping land. Accumulation of aromatic and carboxylic functions on specific spots and marginal co-localization with clays was observed, which suggests processes other than organo-mineral associations being

  6. Confocal Raman microspectroscopy on excised human skin: uncertainties in depth profiling and mathematical correction applied to dermatological drug permeation.

    PubMed

    Tfayli, A; Piot, O; Manfait, M

    2008-05-01

    Confocal Raman microspectroscopy represents the advantage of giving structural and conformational information on samples without any destructive treatment. Recently, several studies were achieved to study the skin hydration, endogenous and exogenous molecules repartition in the skin using the confocal feature of this technique. Meanwhile, when working through a material boundary with a different refractive index, the main limitation remains the spatial precision, especially the distortion in the depth and the depth resolution. Recently, several authors described mathematical models to correct the depth and the resolution values. In this study, we combined theoretical approaches, proposed by different authors with experimental measurements to try to find out the most appropriate approach for correction. We then applied the corrections on in-depth profiles tracking the penetration of Metronidazole, a drug produced by Galderma for rosacea treatment, through excised human skin.

  7. High-contrast Brillouin and Raman micro-spectroscopy for simultaneous mechanical and chemical investigation of microbial biofilms.

    PubMed

    Mattana, S; Alunni Cardinali, M; Caponi, S; Casagrande Pierantoni, D; Corte, L; Roscini, L; Cardinali, G; Fioretto, D

    2017-06-24

    Mechanical mapping with chemical specificity of biological samples is now made possible by joint micro-Brillouin and micro-Raman measurements. In this work, thanks to the unprecedented contrast of a new tandem Fabry-Perot interferometer, we demonstrate simultaneous detection of Brillouin and Raman spectra from different Candida biofilms. Our proof-of-concept study reveals the potential of this label-free joint micro-spectroscopy technique in challenging microbiological issues. In particular, heterogeneous chemo-mechanical maps of Candida biofilms are obtained, without the need for staining or touching the sample. The correlative Raman and Brillouin investigation evidences the role of both extracellular polymeric substances and of hydration water in inducing a marked local softening of the biofilm. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Monitoring the RNA distribution in human embryonic stem cells using Raman micro-spectroscopy and fluorescence imaging

    NASA Astrophysics Data System (ADS)

    Falamas, A.; Kalra, S.; Chis, V.; Notingher, I.

    2013-11-01

    The aim of this study was to monitor the intracellular distribution of nucleic acids in human embryonic stem cells. Raman micro-spectroscopy and fluorescence imaging investigations were employed to obtain high-spatial resolution maps of nucleic acids. The DNA Raman signal was identified based on the 782 cm-1 band, while the RNA characteristic signal was detected based on the 813 cm-1 fingerprint band assigned to O-P-O symmetric stretching vibrations. Additionally, principal components analysis was performed and nucleic acids characteristic Raman signals were identified in the data set, which were plotted at each position in the cells. In this manner, high intensity RNA signal was identified in the cells nucleolus and cytoplasm, while the nucleus presented a much lower signal.

  9. Label-free imaging and quantitative chemical analysis of Alzheimer's disease brain samples with multimodal multiphoton nonlinear optical microspectroscopy.

    PubMed

    Lee, Jang Hyuk; Kim, Dae Hwan; Song, Woo Keun; Oh, Myoung-Kyu; Ko, Do-Kyeong

    2015-05-01

    We developed multimodal multiphoton microspectroscopy using a small-diameter probe with gradient-index lenses and applied it to unstained Alzheimer's disease (AD) brain samples. Our system maintained the image quality and spatial resolution of images obtained using an objective lens of similar numerical aperture. Multicolor images of AD brain samples were obtained simultaneously by integrating two-photon excited fluorescence and second-harmonic generation on a coherent anti-Stokes Raman scattering (CARS) microendoscope platform. Measurements of two hippocampal regions, the cornus ammonis-1 and dentate gyrus, revealed more lipids, amyloid fibers, and collagen in the AD samples than in the normal samples. Normal and AD brains were clearly distinguished by a large spectral difference and quantitative analysis of the CH mode using CARS microendoscope spectroscopy. We expect this system to be an important diagnosis tool in AD research

  10. Label-free imaging and quantitative chemical analysis of Alzheimer's disease brain samples with multimodal multiphoton nonlinear optical microspectroscopy

    NASA Astrophysics Data System (ADS)

    Lee, Jang Hyuk; Kim, Dae Hwan; Song, Woo Keun; Oh, Myoung-Kyu; Ko, Do-Kyeong

    2015-05-01

    We developed multimodal multiphoton microspectroscopy using a small-diameter probe with gradient-index lenses and applied it to unstained Alzheimer's disease (AD) brain samples. Our system maintained the image quality and spatial resolution of images obtained using an objective lens of similar numerical aperture. Multicolor images of AD brain samples were obtained simultaneously by integrating two-photon excited fluorescence and second-harmonic generation on a coherent anti-Stokes Raman scattering (CARS) microendoscope platform. Measurements of two hippocampal regions, the cornus ammonis-1 and dentate gyrus, revealed more lipids, amyloid fibers, and collagen in the AD samples than in the normal samples. Normal and AD brains were clearly distinguished by a large spectral difference and quantitative analysis of the CH mode using CARS microendoscope spectroscopy. We expect this system to be an important diagnosis tool in AD research.

  11. Synchrotron FTIR micro-spectroscopy for structural analysis of Lewy bodies in the brain of Parkinson's disease patients.

    PubMed

    Araki, Katsuya; Yagi, Naoto; Ikemoto, Yuka; Yagi, Hisashi; Choong, Chi-Jing; Hayakawa, Hideki; Beck, Goichi; Sumi, Hisae; Fujimura, Harutoshi; Moriwaki, Taro; Nagai, Yoshitaka; Goto, Yuji; Mochizuki, Hideki

    2015-12-01

    Lewy bodies (LBs), which mainly consist of α-synuclein (α-syn), are neuropathological hallmarks of patients with Parkinson's disease (PD). The fine structure of LBs is unknown, and LBs cannot be made artificially. Nevertheless, many studies have described fibrillisation using recombinant α-syn purified from E. coli. An extremely fundamental problem is whether the structure of LBs is the same as that of recombinant amyloid fibrils. Thus, we used synchrotron Fourier transform infrared micro-spectroscopy (FTIRM) to analyse the fine structure of LBs in the brain of PD patients. Our results showed a shift in the infrared spectrum that indicates abundance of a β-sheet-rich structure in LBs. Also, 2D infrared mapping of LBs revealed that the content of the β-sheet structure is higher in the halo than in the core, and the core contains a large amount of proteins and lipids.

  12. Ultra-structural organisation of cell wall polymers in normal and tension wood of aspen revealed by polarisation FTIR microspectroscopy.

    PubMed

    Olsson, Anne-Mari; Bjurhager, Ingela; Gerber, Lorenz; Sundberg, Björn; Salmén, Lennart

    2011-06-01

    Polarisation Fourier transform infra-red (FTIR) microspectroscopy was used to characterize the organisation and orientation of wood polymers in normal wood and tension wood from hybrid aspen (Populus tremula × Populus tremuloides). It is shown that both xylan and lignin in normal wood are highly oriented in the fibre wall. Their orientation is parallel with the cellulose microfibrils and hence in the direction of the fibre axis. In tension wood a similar orientation of lignin was found. However, in tension wood absorption peaks normally assigned to xylan exhibited a 90° change in the orientation dependence of the vibrations as compared with normal wood. The molecular origin of these vibrations are not known, but they are abundant enough to mask the orientation dependence of the xylan signal from the S₂ layer in tension wood and could possibly come from other pentose sugars present in, or associated with, the gelatinous layer of tension wood fibres.

  13. X27A - A New Hard X-ray Micro-Spectroscopy Facility at the National Synchrtron Light Source

    SciTech Connect

    Ablett,J.; Kao, C.; Reeder, R.; Tang, Y.; Lanzirotti, A.

    2006-01-01

    A new hard X-ray micro-spectroscopy beamline has recently been installed at bending-magnet beamline X27A at the National Synchrotron Light Source, where the focus of research is primarily directed towards the environmental, geological and materials science communities. This instrument delivers moderate, {approx}10 {micro}m spatial resolution using achromatic dynamically bent Kirkpatrick-Baez mirrors, in addition to providing high X-ray flux throughput and selectable energy resolution. The balance between moderate spatial resolution and high flux throughput, in combination with a liquid nitrogen-cooled 13-element energy-dispersive high-purity germanium detector, is particularly well suited to the investigation of dilute and thin-film systems using the fluorescence X-ray absorption fine-structure mode of detection. In this paper, we report on the design and performance of this instrument and highlight a recent experimental study undertaken at this facility.

  14. Electron Microscopy and Raman Microspectroscopy as Characterization Tools and Probes of the Chemistry and Properties of Individual Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Grassian, V. H.

    2012-12-01

    Microscopic probes provide useful insights into the physicochemical properties of aerosol particles and their environmental and health effects. The focus of this talk is on the use of microscopic probes in a wide-range of laboratory studies to better understand the physicochemical properties (chemical heterogeneity, morphology, water uptake, infrared extinction and heterogeneous reactivity) of individual atmospheric aerosol particles. Microscopy coupled to energy dispersive X-ray analysis is used in these studies to characterize particles in terms of size and shape as individual particles or as aggregates particles as well as to follow chemical and physical transformations of particles as they undergo reactions under different environmental conditions. Raman microspectroscopy provides additional chemical specific information and the internal mixing of chemical constituents within individual particles. Several examples will be discussed for flyash, mineral dust and sea spray aerosol particles.

  15. A semi-automated Raman micro-spectroscopy method for morphological and chemical characterizations of microplastic litter.

    PubMed

    L, Frère; I, Paul-Pont; J, Moreau; P, Soudant; C, Lambert; A, Huvet; E, Rinnert

    2016-12-15

    Every step of microplastic analysis (collection, extraction and characterization) is time-consuming, representing an obstacle to the implementation of large scale monitoring. This study proposes a semi-automated Raman micro-spectroscopy method coupled to static image analysis that allows the screening of a large quantity of microplastic in a time-effective way with minimal machine operator intervention. The method was validated using 103 particles collected at the sea surface spiked with 7 standard plastics: morphological and chemical characterization of particles was performed in <3h. The method was then applied to a larger environmental sample (n=962 particles). The identification rate was 75% and significantly decreased as a function of particle size. Microplastics represented 71% of the identified particles and significant size differences were observed: polystyrene was mainly found in the 2-5mm range (59%), polyethylene in the 1-2mm range (40%) and polypropylene in the 0.335-1mm range (42%).

  16. Raman micro-spectroscopy study of living SH-SY5Y cells adhering on different substrates.

    PubMed

    Caponi, S; Mattana, S; Ricci, M; Sagini, K; Urbanelli, L; Sassi, P; Morresi, A; Emiliani, C; Dalla Serra, M; Iannotta, S; Musio, C; Fioretto, D

    2016-01-01

    In this paper we test the ability of Raman micro-spectroscopy and Raman mapping to investigate the status of cells grown in adhesion on different substrates. The spectra of immortalized SH-SY5Y cells, grown on silicon and on metallic substrates are compared with those obtained for the same type of cells adhering on organic polyaniline (PANI), a memristive substrate chosen to achieve a living bio-hybrid system. Raman spectra give information on the status of the single cell, its local biochemical composition, and on the modifications induced by the substrate interaction. The good agreement between Raman spectra collected from cells adhering on different substrates confirms that the PANI, besides allowing the cell growth, doesn't strongly affect the general biochemical properties of the cell. The investigation of the cellular state in a label free condition is challenging and the obtained results confirm the Raman ability to achieve this information.

  17. Localized (5 {mu}m) probing and detailed mapping of hair with synchrotron powered FT-IR microspectroscopy

    SciTech Connect

    Wetzel, David L. Williams, Gwyn P.

    1998-06-01

    The thickness and high absorptivity of single hairs typically result in the saturation of major infrared bands and their distortion. Single human hairs longitudinally microtomed and mounted on mirror slides were scanned routinely in the past with a 20thinsp{mu}m{times}100thinsp{mu}m aperture that limited spatial resolution for localized probing and detailed mapping. Use of the nondivergent, bright, and low-noise synchrotron source for FT-IR microspectroscopy enables good S/N even at apertures as small as 5{endash}6 {mu}m. Functional group mapping as well as localized probing for extraneous materials illustrates the utility of this powerful probe. {copyright} {ital 1998 American Institute of Physics.}

  18. Local observation of modes from three-dimensional woodpile photonic crystals with near-field microspectroscopy under supercontinuum illumination.

    PubMed

    Jia, Baohua; Norton, Andrew H; Li, Jiafang; Rahmani, Adel; Asatryan, Ara A; Botten, Lindsay C; Gu, Min

    2008-05-15

    A near-field microscope coupled with a near-infrared (NIR) supercontinuum source is developed and applied to characterize optical modes in a three-dimensional (3D) woodpile photonic crystal (PC) possessing a NIR partial bandgap. Spatially resolved near-field intensity distributions under different illumination wavelengths demonstrate that the electric fields preferentially dwell in the polymer rods or in the gaps between rods, respectively, for frequencies below or above the stop gap, as predicted by the 3D finite-difference time-domain modeling. Near-field microspectroscopy further reveals that the position-dependent band-edge effect plays an important role in PC-based all-optical integrated devices.

  19. Synchrotron FTIR micro-spectroscopy for structural analysis of Lewy bodies in the brain of Parkinson’s disease patients

    NASA Astrophysics Data System (ADS)

    Araki, Katsuya; Yagi, Naoto; Ikemoto, Yuka; Yagi, Hisashi; Choong, Chi-Jing; Hayakawa, Hideki; Beck, Goichi; Sumi, Hisae; Fujimura, Harutoshi; Moriwaki, Taro; Nagai, Yoshitaka; Goto, Yuji; Mochizuki, Hideki

    2015-12-01

    Lewy bodies (LBs), which mainly consist of α-synuclein (α-syn), are neuropathological hallmarks of patients with Parkinson’s disease (PD). The fine structure of LBs is unknown, and LBs cannot be made artificially. Nevertheless, many studies have described fibrillisation using recombinant α-syn purified from E. coli. An extremely fundamental problem is whether the structure of LBs is the same as that of recombinant amyloid fibrils. Thus, we used synchrotron Fourier transform infrared micro-spectroscopy (FTIRM) to analyse the fine structure of LBs in the brain of PD patients. Our results showed a shift in the infrared spectrum that indicates abundance of a β-sheet-rich structure in LBs. Also, 2D infrared mapping of LBs revealed that the content of the β-sheet structure is higher in the halo than in the core, and the core contains a large amount of proteins and lipids.

  20. Thermal stability and molecular microstructure of heat-induced cereal grains, revealed with Raman molecular microspectroscopy and differential scanning calorimetry.

    PubMed

    Khan, Md Majibur Rahman; Yu, Peiqiang

    2013-07-03

    The objectives of the present study were to use Raman molecular microspectroscopy and differential scanning calorimetry (DSC) to reveal molecular thermal stability and thermal degradation behavior of heat-induced cereal grains and reveal the molecular chemistry of the protein structures of cereal grain tissues affected by heat processing and to quantify the protein secondary structures using multicomponent peak modeling Gaussian and Lorentzian methods. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were also conducted to identify molecular differences in the Raman spectra. Three cereal grain seeds, wheat, triticale, and corn, were used as the model for feed protein in the experiment. The specimens were autoclaved (moist heating) and dry-heated (roasted) at 121 °C for 80 min, respectively. Raman spectroscopy results revealed that there are marked differences in the secondary structures of the proteins subjected to various heating treatments of different cereals. The sensitivity of cereals to moist heating was much higher than the sensitivity to dry heating. The multivariate analyses (CLA and PCA) showed that heat treatment was significantly isolated between the different Raman raw spectra. The DSC study revealed that the thermal degradation behavior of cereals was significantly changed after moist- and dry-heat treatments. The position of the major endothermic peak of dry-heated cereals shifted toward a higher temperature, from 131.7 to 134.0 °C, suggesting the high thermal stability of dry-heated cereals. In contrast, the endothermic peak position was slightly decreased to 132.1 °C in the case of moist autoclaved heating. The digestive behavior and nutritive value of rumen-undegradable protein in animals may be related to the changes of the protein secondary molecular structure and thermal stability of the cereal grain materials, which is attributed by Raman microspectroscopy and DSC endotherm profiles.

  1. Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Sackett, O.; Armand, L.; Beardall, J.; Hill, R.; Doblin, M.; Connelly, C.; Howes, J.; Stuart, B.; Ralph, P.; Heraud, P.

    2014-05-01

    Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value, furthermore data on taxon-specific responses is almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate and carbohydrates. In contrast to some previous studies, silicate levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community measurements, highlighting the

  2. Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy

    NASA Astrophysics Data System (ADS)

    Sackett, O.; Armand, L.; Beardall, J.; Hill, R.; Doblin, M.; Connelly, C.; Howes, J.; Stuart, B.; Ralph, P.; Heraud, P.

    2014-10-01

    Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value - furthermore, data on taxon-specific responses are almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate/silicic acid and carbohydrates. In contrast to some previous studies, silicate/silicic acid levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community

  3. Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Liu, Jinghua; Qi, Zeming; Huang, Qing; Wei, Xiaoli; Ke, Zhigang; Fang, Yusheng; Tian, Yangchao; Yu, Zengliang

    2013-01-01

    Energetic particles exist ubiquitously and cause varied biological effects such as DNA strand breaks, lipid peroxidation, protein modification, cell apoptosis or death. An emerging biotechnology based on ion-beam technique has been developed to serve as an effective tool for mutation breeding of crops and microbes. In order to improve the effectiveness of ion-beam biotechnology for mutation breeding, it is indispensible to gain a better understanding of the mechanism of the interactions between the energetic ions and biological systems which is still elusive. A new trend is to conduct more comprehensive research which is based on micro-scaled observation of the changes of the cellular structures and compositions under the interactions. For this purpose, advanced synchrotron FTIR (s-FTIR) microscopy was employed to monitor the cellular changes of single fungal hyphae under irradiation of α-particles from 241Am. Intracellular contents of ROS, MDA, GSSG/GSH and activities of CAT and SOD were measured via biochemical assay. Ion-irradiation on Rhizopus oryzae causes localized vacuolation, autolysis of cell wall and membrane, lipid peroxidation, DNA damage and conformational changes of proteins, which have been clearly revealed by the s-FTIR microspectroscopy. The different changes of cell viability, SOD and CAT activities can be explained by the ROS-involved chemical reactions. Evidently, the elevated level of ROS in hyphal cells upon irradiation plays the key role in the caused biological effect. This study demonstrates that s-FTIR microspectroscopy is an effective tool to study the damage of fungal hyphae caused by ionizing radiation and it facilitates the exploit of the mechanism for the interactions between the energetic ions and biological systems.

  4. From the meso to the nanoscopic scale through synchrotron imaging approaches: advances and near future at the NSLS-II SRX beamline

    NASA Astrophysics Data System (ADS)

    De Andrade, V.; Thieme, J.; Ganne, J.; Beck, P.; Fayard, B.; Salomé, M.

    2012-12-01

    instrument for Earth Sciences. SRX is one of the first 6 project beamlines of the new National Synchrotron Light Source II (NSLS-II). Operating from 4.65 to 28 keV, SRX will comprise a high flux station and a nanoprobe (switchable within a couple of minutes), both operating with a world leading flux. SRX will start early science experiments in spring 2014. References [1] De Andrade, V., Susini, et al., "Submicrometer Hyperspectral X-ray Imaging of Heterogeneous Rocks and Geomaterials: Applications at the Fe K-Edge," Analytical Chemistry, 83(11), 4220-4227 (2011). [2] Beck P., De Andrade V., et al., "The redox state of iron in the matrix of CI, CM and metamorphosed CM chondrites by XANES spectroscopy". In press GCA. [3] Ganne J., De Andrade, et al., "Modern-style plate subduction and HP-LT rocks preserved in the Palaeoproterozoic West African Craton," Nature Geosciences, 5, 60-65, (2012). [4] De Andrade V., Thieme, J, et al., "The sub-micron resolution X-ray spectroscopy beamline at NSLS-II", Nuclear Instruments and Methods in Physics Research Section A, 649(1), 46-48 (2011).

  5. Microstrain distribution mapping on CuInSe2 thin films by means of electron backscatter diffraction, X-ray diffraction, and Raman microspectroscopy.

    PubMed

    Schäfer, Norbert; Wilkinson, Angus J; Schmid, Thomas; Winkelmann, Aimo; Chahine, Gilbert A; Schülli, Tobias U; Rissom, Thorsten; Marquardt, Julien; Schorr, Susan; Abou-Ras, Daniel

    2016-10-01

    The investigation of the microstructure in functional, polycrystalline thin films is an important contribution to the enhanced understanding of structure-property relationships in corresponding devices. Linear and planar defects within individual grains may affect substantially the performance of the device. These defects are closely related to strain distributions. The present work compares electron and X-ray diffraction as well as Raman microspectroscopy, which provide access to microstrain distributions within individual grains. CuInSe2 thin films for solar cells are used as a model system. High-resolution electron backscatter diffraction and X-ray microdiffraction as well as Raman microspectroscopy were applied for this comparison. Consistently, microstrain values were determined of the order of 10(-4) by these three techniques. However, only electron backscatter diffraction, X-ray microdiffraction exhibit sensitivities appropriate for mapping local strain changes at the submicrometer level within individual grains in polycrystalline materials. Copyright © 2016 Elsevier B.V. All rights reserved.

  6. Synchrotron-based FTIR microspectroscopy for the mapping of photo-oxidation and additives in acrylonitrile-butadiene-styrene model samples and historical objects.

    PubMed

    Saviello, Daniela; Pouyet, Emeline; Toniolo, Lucia; Cotte, Marine; Nevin, Austin

    2014-09-16

    Synchrotron-based Fourier transform infrared micro-spectroscopy (SR-μFTIR) was used to map photo-oxidative degradation of acrylonitrile-butadiene-styrene (ABS) and to investigate the presence and the migration of additives in historical samples from important Italian design objects. High resolution (3×3 μm(2)) molecular maps were obtained by FTIR microspectroscopy in transmission mode, using a new method for the preparation of polymer thin sections. The depth of photo-oxidation in samples was evaluated and accompanied by the formation of ketones, aldehydes, esters, and unsaturated carbonyl compounds. This study demonstrates selective surface oxidation and a probable passivation of material against further degradation. In polymer fragments from design objects made of ABS from the 1960s, UV-stabilizers were detected and mapped, and microscopic inclusions of proteinaceous material were identified and mapped for the first time.

  7. One-step simultaneous differential scanning calorimetry-FTIR microspectroscopy to quickly detect continuous pathways in the solid-state glucose/asparagine Maillard reaction.

    PubMed

    Hwang, Deng-Fwu; Hsieh, Tzu-Feng; Lin, Shan-Yang

    2013-01-01

    The stepwise reaction pathway of the solid-state Maillard reaction between glucose (Glc) and asparagine (Asn) was investigated using simultaneous differential scanning calorimetry (DSC)-FTIR microspectroscopy. The color change and FTIR spectra of Glc-Asn physical mixtures (molar ratio = 1:1) preheated to different temperatures followed by cooling were also examined. The successive reaction products such as Schiff base intermediate, Amadori product, and decarboxylated Amadori product in the solid-state Glc-Asn Maillard reaction were first simultaneously evidenced by this unique DSC-FTIR microspectroscopy. The color changed from white to yellow-brown to dark brown, and appearance of new IR peaks confirmed the formation of Maillard reaction products. The present study clearly indicates that this unique DSC-FTIR technique not only accelerates but also detects precursors and products of the Maillard reaction in real time.

  8. Characterization and analysis of mycobacteria and Gram-negative bacteria and co-culture mixtures by Raman microspectroscopy, FTIR, and atomic force microscopy.

    PubMed

    Tang, Mingjie; McEwen, Gerald D; Wu, Yangzhe; Miller, Charles D; Zhou, Anhong

    2013-02-01

    The molecular composition of mycobacteria and Gram-negative bacteria cell walls is structurally different. In this work, Raman microspectroscopy was applied to discriminate mycobacteria and Gram-negative bacteria by assessing specific characteristic spectral features. Analysis of Raman spectra indicated that mycobacteria and Gram-negative bacteria exhibit different spectral patterns under our experimental conditions due to their different biochemical components. Fourier transform infrared (FTIR) spectroscopy, as a supplementary vibrational spectroscopy, was also applied to analyze the biochemical composition of the representative bacterial strains. As for co-cultured bacterial mixtures, the distribution of individual cell types was obtained by quantitative analysis of Raman and FTIR spectral images and the spectral contribution from each cell type was distinguished by direct classical least squares analysis. Coupled atomic force microscopy (AFM) and Raman microspectroscopy realized simultaneous measurements of topography and spectral images for the same sampled surface. This work demonstrated the feasibility of utilizing a combined Raman microspectroscopy, FTIR, and AFM techniques to effectively characterize spectroscopic fingerprints from bacterial Gram types and mixtures.

  9. Raman microspectroscopy as a diagnostic tool for the non-invasive analysis of fibrillin-1 deficiency in the skin and in the in vitro skin models.

    PubMed

    Brauchle, Eva; Bauer, Hannah; Fernes, Patrick; Zuk, Alexandra; Schenke-Layland, Katja; Sengle, Gerhard

    2017-04-01

    Fibrillin microfibrils and elastic fibers are critical determinants of elastic tissues where they define as tissue-specific architectures vital mechanical properties such as pliability and elastic recoil. Fibrillin microfibrils also facilitate elastic fiber formation and support the association of epithelial cells with the interstitial matrix. Mutations in fibrillin-1 (FBN1) are causative for the Marfan syndrome, a congenital multisystem disorder characterized by progressive deterioration of the fibrillin microfibril/ elastic fiber architecture in the cardiovascular, musculoskeletal, ocular, and dermal system. In this study, we utilized Raman microspectroscopy in combination with principal component analysis (PCA) to analyze the molecular consequences of fibrillin-1 deficiency in skin of a mouse model (GT8) of Marfan syndrome. In addition, full-thickness skin models incorporating murine wild-type and Fbn1(GT8/GT8) fibroblasts as well as human HaCaT keratinocytes were generated and analyzed. Skin models containing GT8 fibroblasts showed an altered epidermal morphology when compared to wild-type models indicating a new role for fibrillin-1 in dermal-epidermal crosstalk. Obtained Raman spectra together with PCA allowed to discriminate between healthy and deficient microfibrillar networks in murine dermis and skin models. Interestingly, results obtained from GT8 dermis and skin models showed similar alterations in molecular signatures triggered by fibrillin-1 deficiency such as amide III vibrations and decreased levels of glycan vibrations. Overall, this study indicates that Raman microspectroscopy has the potential to analyze subtle changes in fibrillin-1 microfibrils and elastic fiber networks. Therefore Raman microspectroscopy may be utilized as a non-invasive and sensitive diagnostic tool to identify connective tissue disorders and monitor their disease progression. Mutations in building blocks of the fibrillin microfibril/ elastic fiber network manifest in disease

  10. Recent applications and current trends in Cultural Heritage Science using synchrotron-based Fourier transform infrared micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Cotte, Marine; Dumas, Paul; Taniguchi, Yoko; Checroun, Emilie; Walter, Philippe; Susini, Jean

    2009-09-01

    Synchrotron-based Fourier transform infrared micro-spectroscopy (SR-FTIR) is one of the emerging techniques increasingly employed for Cultural Heritage analytical science. Such a technique combines the assets of FTIR spectroscopy (namely, the identification of molecular groups in various environments: organic/inorganic, crystallized/amorphous, solid/liquid/gas), with the extra potential of chemical imaging (localization of components + easier data treatment thanks to geographical correlations) and the properties of the synchrotron source (namely, high brightness, offering high data quality even with reduced dwell time and reduced spot size). This technique can be applied to nearly all kind of materials found in museum objects, going from hard materials, like metals, to soft materials, like paper, and passing through hybrid materials such as paintings and bones. The purpose is usually the identification of complex compositions in tiny, heterogeneous samples. Recent applications are reviewed in this article, together with the fundamental aspects of the infrared synchrotron source which are leading to such improvements in analytical capabilities. A recent example from the ancient Buddhist paintings from Bamiyan is detailed. Emphasis is made on the true potential offered at such large scale facilities in combining SR-FTIR microscopy with other synchrotron-based micro-imaging techniques. To cite this article: M. Cotte et al., C. R. Physique 10 (2009).

  11. Rapid analysis of two food-borne microbial communities at the species level by Fourier-transform infrared microspectroscopy.

    PubMed

    Wenning, Mareike; Theilmann, Vera; Scherer, Siegfried

    2006-05-01

    The species composition of microbial communities in natural habitats may be extremely complex and therefore a quantitative analysis of the fraction each species contributes to the consortium has proven to be difficult. During recent years, the identification of bacterial pure cultures based on their infrared spectra has been established. Fourier-transform infrared microspectroscopy now proceeds a step further and allows identification of microorganisms directly plated from community dilutions. Infrared spectra of microcolonies of 70-250 microm in diameter can be recorded without producing a pure culture of the isolate. We have applied this novel technique for quantitative comparative analysis of two undefined, geographically separated food-borne smear cheese microbial consortia of limited complexity. Due to the high degree of automation, up to 200 microcolonies could be identified in 1 day and, in total, 3170 infrared spectra of microcolonies were recorded. The results obtained have been verified by Fourier-transform infrared macrospectroscopy and 16S rDNA sequencing. Interestingly, although the communities were unrelated, Staphylococcus equorum, Corynebacterium casei, Arthrobacter casei and Brevibacterium linens were found to be part of both consortia, however, with different incidence. In addition, Corynebacterium variabile, Microbacterium gubbeenense, Brachybacterium alimentarium, Enterococcus faecalis and an unknown species were detected in either one of the consortia.

  12. Soot Structure and Reactivity Analysis by Raman Microspectroscopy, Temperature-Programmed Oxidation, and High-Resolution Transmission Electron Microscopy

    NASA Astrophysics Data System (ADS)

    Knauer, Markus; Schuster, Manfred E.; Su, Dangsheng; Schlögl, Robert; Niessner, Reinhard; Ivleva, Natalia P.

    2009-11-01

    Raman microspectroscopy (RM), temperature-programmed oxidation (TPO), high-resolution transmission electron microscopy (HRTEM), and electron energy loss spectroscopy (EELS) were combined to get comprehensive information on the relationship between structure and reactivity of soot in samples of spark discharge (GfG), heavy duty engine diesel (EURO VI and IV) soot, and graphite powder upon oxidation by oxygen at increasing temperatures. GfG soot and graphite powder represent the higher and lower reactivity limits. Raman microspectroscopic analysis was conducted by determination of spectral parameters using a five band fitting procedure (G, D1-D4) as well as by evaluation of the dispersive character of the D mode. The analysis of spectral parameters shows a higher degree of disorder and a higher amount of molecular carbon for untreated GfG soot samples than for samples of untreated EURO VI and EURO IV soot. The structural analysis based on the dispersive character of the D mode revealed substantial differences in ordering descending from graphite powder, EURO IV, VI to GfG soot. HRTEM images and EELS analysis of EURO IV and VI samples indicated a different morphology and a higher structural order as compared to GfG soot in full agreement with the Raman analysis. These findings are also confirmed by the reactivity of soot during oxidation (TPO), where GfG soot was found to be the most reactive and EURO IV and VI soot samples exhibited a moderate reactivity.

  13. The use of synchrotron infrared microspectroscopy in the assessment of cutaneous T-cell lymphoma vs. pityriasis lichenoides chronica.

    PubMed

    El Bedewi, Ahmed; El Anany, Galal; El Mofty, Medhat; Kretlow, Ariane; Park, Simone; Miller, Lisa M

    2010-04-01

    The diagnosis of cutaneous lymphomas remains a challenge for both the clinician and dermatopathologist. To differentiate between frank malignant and premalignant lymphocytes within the skin. This study was performed on 20 patients with a mean age of 50 years. They were divided into two groups: mycosis fungoides (MF) (stage IA, IB and IIA) and pityriasis lichenoides chronica (PLC). Immunophenotyping using antibodies CD3, CD4, CD8, CD20 and CD30 was performed. Synchrotron Fourier transform infrared microspectroscopy (S-FTIRM) was performed on cell nuclei to assess chemical differences between MF and PLC cases as a potential complementary screening tool. Dermal spectra of both MF and PLC were compared using principal components analysis (PCA) of the S-FTIRM data. All PLC spectra was clustered together. However, the MF spectra formed two clusters, one that grouped with the PLC and the other grouped separately. Moreover, protein and nucleic acids showed highly significant differences between MF (IIA and IB), MF (IA) and PLC. The malignant transformation within lymphocytes was identifiable through the spectroscopic analysis of protein, RNA and DNA with S-FTIRM, making it a promising tool for classifying the progression of cutaneous T-cell lymphoma.

  14. Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time.

    PubMed

    Hall, Edward K; Singer, Gabriel A; Pölzl, Marvin; Hämmerle, Ieda; Schwarz, Christian; Daims, Holger; Maixner, Frank; Battin, Tom J

    2011-02-01

    Stoichiometry of microbial biomass is a key determinant of nutrient recycling in a wide variety of ecosystems. However, little is known about the underlying causes of variance in microbial biomass stoichiometry. This is primarily because of technological constraints limiting the analysis of macromolecular composition to large quantities of microbial biomass. Here, we use Raman microspectroscopy (MS), to analyze the macromolecular composition of single cells of two species of bacteria grown on minimal media over a wide range of resource stoichiometry. We show that macromolecular composition, determined from a subset of identified peaks within the Raman spectra, was consistent with macromolecular composition determined using traditional analytical methods. In addition, macromolecular composition determined by Raman MS correlated with total biomass stoichiometry, indicating that analysis with Raman MS included a large proportion of a cell's total macromolecular composition. Growth phase (logarithmic or stationary), resource stoichiometry and species identity each influenced each organism's macromolecular composition and thus biomass stoichiometry. Interestingly, the least variable peaks in the Raman spectra were those responsible for differentiation between species, suggesting a phylogenetically specific cellular architecture. As Raman MS has been previously shown to be applicable to cells sampled directly from complex environments, our results suggest Raman MS is an extremely useful application for evaluating the biomass stoichiometry of environmental microorganisms. This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity.

  15. Infrared Microspectroscopy: A Multiple-Screening Platform for Investigating Single-Cell Biochemical Perturbations upon Prion Infection

    PubMed Central

    2011-01-01

    Prion diseases are a group of fatal neurodegenerative disorders characterized by the accumulation of prions in the central nervous system. The pathogenic prion (PrPSc) possesses the capability to convert the host-encoded cellular isoform of the prion protein, PrPC, into nascent PrPSc. The present work aims at providing novel insight into cellular response upon prion infection evidenced by synchrotron radiation infrared microspectroscopy (SR-IRMS). This non-invasive, label-free analytical technique was employed to investigate the biochemical perturbations undergone by prion infected mouse hypothalamic GT1-1 cells at the cellular and subcellular level. A decrement in total cellular protein content upon prion infection was identified by infrared (IR) whole-cell spectra and validated by bicinchoninic acid assay and single-cell volume analysis by atomic force microscopy (AFM). Hierarchical cluster analysis (HCA) of IR data discriminated between infected and uninfected cells and allowed to deduce an increment of lysosomal bodies within the cytoplasm of infected GT1-1 cells, a hypothesis further confirmed by SR-IRMS at subcellular spatial resolution and fluorescent microscopy. The purpose of this work, therefore, consists of proposing IRMS as a powerful multiscreening platform, drawing on the synergy with conventional biological assays and microscopy techniques in order to increase the accuracy of investigations performed at the single-cell level. PMID:22778865

  16. Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time

    USGS Publications Warehouse

    Hall, Edward K.; Singer, Gabriel A.; Pölzl, Marvin; Hämmerle, Ieda; Schwarz, Christian; Daims, Holger; Maixner, Frank; Battin, Tom J.

    2011-01-01

    Stoichiometry of microbial biomass is a key determinant of nutrient recycling in a wide variety of ecosystems. However, little is known about the underlying causes of variance in microbial biomass stoichiometry. This is primarily because of technological constraints limiting the analysis of macromolecular composition to large quantities of microbial biomass. Here, we use Raman microspectroscopy (MS), to analyze the macromolecular composition of single cells of two species of bacteria grown on minimal media over a wide range of resource stoichiometry. We show that macromolecular composition, determined from a subset of identified peaks within the Raman spectra, was consistent with macromolecular composition determined using traditional analytical methods. In addition, macromolecular composition determined by Raman MS correlated with total biomass stoichiometry, indicating that analysis with Raman MS included a large proportion of a cell's total macromolecular composition. Growth phase (logarithmic or stationary), resource stoichiometry and species identity each influenced each organism's macromolecular composition and thus biomass stoichiometry. Interestingly, the least variable peaks in the Raman spectra were those responsible for differentiation between species, suggesting a phylogenetically specific cellular architecture. As Raman MS has been previously shown to be applicable to cells sampled directly from complex environments, our results suggest Raman MS is an extremely useful application for evaluating the biomass stoichiometry of environmental microorganisms. This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity.

  17. Soft X-ray induced modifications of PVA-based microbubbles in aqueous environment: a microspectroscopy study.

    PubMed

    Tzvetkov, George; Fernandes, Paulo; Wenzel, Stephan; Fery, Andreas; Paradossi, Gaio; Fink, Rainer H

    2009-02-21

    We use scanning-transmission X-ray microspectroscopy (STXM) for in situ characterization of the physicochemical changes in air-filled poly(vinyl alcohol) (PVA) based microbubbles upon soft X-ray irradiation. The microbubbles were illuminated directly in aqueous suspension with 520 eV X-rays and a continuous shrinkage of the particles with an illumination time/radiation dose was observed. Utilizing the intrinsic absorption properties of the species and the high spatial resolution of the STXM, the modifications of the particles' structure were simultaneously recognized. A thorough characterization of the microbubble volume, membrane thickness and absorption coefficient was performed by quantitative fitting of the radial transmittance profiles of the targeted microbubbles. Apart from the observed volume contraction, there was no significant change in the shell thickness. The chemical changes in the membranes were clarified via C K-edge near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. It was revealed that the observed structural alterations go along with a continuous degradation of the PVA network associated with formation of carbonyl- and carboxyl-containing species as well as an increased content of unsaturated bonds.

  18. Assessment of metabolic modulation in free-living versus endosymbiotic Symbiodinium using synchrotron radiation-based infrared microspectroscopy

    PubMed Central

    Peng, Shao-En; Chen, Chii-Shiarng; Song, Yen-Fang; Huang, Huai-Ting; Jiang, Pei-Luen; Chen, Wan-Nan U.; Fang, Lee-Shing; Lee, Yao-Chang

    2012-01-01

    The endosymbiotic relationship between coral hosts and dinoflagellates of the genus Symbiodinium is critical for the growth and productivity of coral reef ecosystems. Here, synchrotron radiation-based infrared microspectroscopy was applied to examine metabolite concentration differences between endosymbiotic (within the anemone Aiptasia pulchella) and free-living Symbiodinium over the light–dark cycle. Significant differences in levels of lipids, nitrogenous compounds, polysaccharides and putative cell wall components were documented. Compared with free-living Symbiodinium, total lipids, unsaturated lipids and polysaccharides were relatively enriched in endosymbiotic Symbiodinium during both light and dark photoperiods. Concentrations of cell wall-related metabolites did not vary temporally in endosymbiotic samples; in contrast, the concentrations of these metabolites increased dramatically during the dark photoperiod in free-living samples, possibly reflecting rhythmic cell-wall synthesis related to light-driven cell proliferation. The level of nitrogenous compounds in endosymbiotic cells did not vary greatly across the light–dark cycle and in general was significantly lower than that observed in free-living samples collected during the light. Collectively, these data suggest that nitrogen limitation is a factor that the host cell exploits to induce the biosynthesis of lipids and polysaccharides in endosymbiotic Symbiodinium. PMID:22090199

  19. Imaging of Osteoarthritic Human Articular Cartilage using Fourier Transform Infrared Microspectroscopy Combined with Multivariate and Univariate Analysis.

    PubMed

    Oinas, J; Rieppo, L; Finnilä, M A J; Valkealahti, M; Lehenkari, P; Saarakkala, S

    2016-07-21

    The changes in chemical composition of human articular cartilage (AC) caused by osteoarthritis (OA) were investigated using Fourier transform infrared microspectroscopy (FTIR-MS). We demonstrate the sensitivity of FTIR-MS for monitoring compositional changes that occur with OA progression. Twenty-eight AC samples from tibial plateaus were imaged with FTIR-MS. Hyperspectral images of all samples were combined for K-means clustering. Partial least squares regression (PLSR) analysis was used to compare the spectra with the OARSI grade (histopathological grading of OA). Furthermore, the amide I and the carbohydrate regions were used to estimate collagen and proteoglycan contents, respectively. Spectral peak at 1338 cm(-1) was used to estimate the integrity of the collagen network. The layered structure of AC was revealed using the carbohydrate region for clustering. Statistically significant correlation was observed between the OARSI grade and the collagen integrity in the superficial (r = -0.55) and the deep (r = -0.41) zones. Furthermore, PLSR models predicted the OARSI grade from the superficial (r = 0.94) and the deep (r = 0.77) regions of the AC with high accuracy. Obtained results suggest that quantitative and qualitative changes occur in the AC composition during OA progression, and these can be monitored by the use of FTIR-MS.

  20. Screening of Astaxanthin-Hyperproducing Haematococcus pluvialis Using Fourier Transform Infrared (FT-IR) and Raman Microspectroscopy.

    PubMed

    Liu, Jinghua; Huang, Qing

    2016-06-13

    Haematococcus pluvialis has promising applications owing to its ability to accumulate astaxanthin under stress conditions. In order to acquire higher astaxanthin productivity from H. pluvialis, it is critical not only to develop efficient mutagenesis techniques, but also to establish rapid and effective screening methods which are highly demanded in current research and application practice. In this work, we therefore attempted to develop a new approach to screening the astaxanthin-hyperproducing strains based on spectroscopic tools. Using Fourier transform infrared (FT-IR) and Raman microspectroscopy, we have achieved rapid and quantitative analysis of the algal cells in terms of astaxanthin, β-carotene, proteins, lipids, and carbohydrates. In particular, we have found that the ratio of the IR absorption band at 1740 cm(-1) to the band at 1156 cm(-1) can be utilized for identifying astaxanthin-hyperproducing strains. This work may therefore open a new avenue for developing high-throughput screening methods necessary for the microbial mutant breeding industry.

  1. Advances in simultaneous DSC-FTIR microspectroscopy for rapid solid-state chemical stability studies: some dipeptide drugs as examples.

    PubMed

    Lin, Shan-Yang; Wang, Shun-Li

    2012-04-01

    The solid-state chemistry of drugs has seen growing importance in the pharmaceutical industry for the development of useful API (active pharmaceutical ingredients) of drugs and stable dosage forms. The stability of drugs in various solid dosage forms is an important issue because solid dosage forms are the most common pharmaceutical formulation in clinical use. In solid-state stability studies of drugs, an ideal accelerated method must not only be selected by different complicated methods, but must also detect the formation of degraded product. In this review article, an analytical technique combining differential scanning calorimetry and Fourier-transform infrared (DSC-FTIR) microspectroscopy simulates the accelerated stability test, and simultaneously detects the decomposed products in real time. The pharmaceutical dipeptides aspartame hemihydrate, lisinopril dihydrate, and enalapril maleate either with or without Eudragit E were used as testing examples. This one-step simultaneous DSC-FTIR technique for real-time detection of diketopiperazine (DKP) directly evidenced the dehydration process and DKP formation as an impurity common in pharmaceutical dipeptides. DKP formation in various dipeptides determined by different analytical methods had been collected and compiled. Although many analytical methods have been applied, the combined DSC-FTIR technique is an easy and fast analytical method which not only can simulate the accelerated drug stability testing but also at the same time enable to explore phase transformation as well as degradation due to thermal-related reactions. This technique offers quick and proper interpretations.

  2. The excitation intensity dependence of singlet fission dynamics of a rubrene microcrystal studied by femtosecond transient microspectroscopy.

    PubMed

    Ishibashi, Y; Inoue, Y; Asahi, T

    2016-10-05

    We have investigated the excitation intensity dependence of the singlet fission in a crystalline rubrene by means of femtosecond transient absorption microspectroscopy. When a rubrene microcrystal was excited to higher energy levels than that of the lowest singlet excited (S1) state with a 397 nm femtosecond laser pulse, a triplet excited state was formed through two pathways of the singlet fission, i.e. the direct fission from higher vibrational levels of the S1 state with a time constant of 2.2 ps and the thermally activated fission from the S1 state in a few tens of ps. The time constant of the thermally activated fission changed from 35 to 17 ps for increasing of the laser fluence from 0.65 to 18 mJ cm(-2) per pulse, although that of the direct fission was constant with the excitation laser intensity. On the other hand, the yield of the triplet formation was independent of the intensity. We also examined the temperature dependence of the singlet fission and demonstrated the activation energy of the thermally activated fission to be 0.21 eV. Based on the experimental results, we considered the excitation intensity dependence of the singlet fission of the rubrene crystal in terms of the effect of transient local heating on a ps time scale after femtosecond laser excitation owing to the nonradiative vibrational relaxation from the higher vibrational level to the lower one in the S1 state.

  3. Direct analysis of water content and movement in single dormant bacterial spores using confocal Raman microspectroscopy and Raman imaging.

    PubMed

    Kong, Lingbo; Setlow, Peter; Li, Yong-qing

    2013-08-06

    Heavy water (D2O) has a distinct molecular vibration spectrum, and this has been used to analyze the water content, distribution, and movement in single dormant Bacillus cereus spores using confocal Raman microspectroscopy and Raman imaging. These methods have been used to measure the kinetics of D2O release from spores suspended in H2O, the spatial distribution of D2O in spores, and the kinetics of D2O release from spores during dehydration in air at room temperature. The results obtained were as follows. (1) The Raman spectrum of single D2O-loaded dormant spores suggests that D2O in spores is in a relatively weak hydrogen-bonded mode, compared to the strong hydrogen-bonded mode in pure D2O. (2) The D2O content of individual spores in a population was somewhat heterogeneous. (3) The spatial distribution of D2O in single dormant spores is uneven, and is less dense in the central core region. Raman images of different molecular components indicate that the water distribution is somewhat different from those of proteins and Ca-dipicolinic acid. (4) Exchange of spore D2O with external H2O took place in less than 1 s. (5) However, release of spore D2O during air dehydration at room temperature was slow and heterogeneous and took 2-3 h for complete D2O release.

  4. Chemical changes demonstrated in cartilage by synchrotron infrared microspectroscopy in an antibody-induced murine model of rheumatoid arthritis

    NASA Astrophysics Data System (ADS)

    Croxford, Allyson M.; Selva Nandakumar, Kutty; Holmdahl, Rikard; Tobin, Mark J.; McNaughton, Don; Rowley, Merrill J.

    2011-06-01

    Collagen antibody-induced arthritis develops in mice following passive transfer of monoclonal antibodies (mAbs) to type II collagen (CII) and is attributed to effects of proinflammatory immune complexes, but transferred mAbs may react directly and damagingly with CII. To determine whether such mAbs cause cartilage damage in vivo in the absence of inflammation, mice lacking complement factor 5 that do not develop joint inflammation were injected intravenously with two arthritogenic mAbs to CII, M2139 and CIIC1. Paws were collected at day 3, decalcified, paraffin embedded, and 5-μm sections were examined using standard histology and synchrotron Fourier-transform infrared microspectroscopy (FTIRM). None of the mice injected with mAb showed visual or histological evidence of inflammation but there were histological changes in the articular cartilage including loss of proteoglycan and altered chondrocyte morphology. Findings using FTIRM at high lateral resolution revealed loss of collagen and the appearance of a new peak at 1635 cm-1 at the surface of the cartilage interpreted as cellular activation. Thus, we demonstrate the utility of synchrotron FTIRM for examining chemical changes in diseased cartilage at the microscopic level and establish that arthritogenic mAbs to CII do cause cartilage damage in vivo in the absence of inflammation.

  5. Determination of spectral markers of cytotoxicity and genotoxicity using in vitro Raman microspectroscopy: cellular responses to polyamidoamine dendrimer exposure.

    PubMed

    Efeoglu, Esen; Casey, Alan; Byrne, Hugh J

    2017-09-12

    Although consumer exposure to nanomaterials is ever increasing, with potential increased applications in areas such as drug and/or gene delivery, contrast agents and diagnosis, the determination of the cyto- and geno-toxic effects of nanomaterials on human health and the environment still remains challenging. Although many techniques have been established and adapted to determine the cytotoxicity and genotoxicity of nano-sized materials, these techniques remain limited by the number of assays required, total cost, and use of labels and they struggle to explain the underlying interaction mechanisms. In this study, Raman microspectroscopy is employed as an in vitro label-free, high content screening technique to observe toxicological changes within the cell in a multi-parametric fashion. The evolution of spectral markers as a function of time and applied dose has been used to elucidate the mechanism of action of polyamidoamine (PAMAM) dendrimers associated with cytotoxicity and their impact on nuclear biochemistry. PAMAM dendrimers are chosen as a model nanomaterial due to their widely studied cytotoxic and genotoxic properties and commercial availability. Point spectra were acquired from the cytoplasm to monitor the cascade of toxic events occurring in the cytoplasm upon nanoparticle exposure, whereas the spectra acquired from the nucleus and the nucleolus were used to explore PAMAM-nuclear material interaction as well as genotoxic responses.

  6. A novel ATR FT-IR microspectroscopy technique for surface contamination analysis without interference of the substrate.

    PubMed

    Ekgasit, Sanong; Pattayakorn, Narumon; Tongsakul, Duangta; Thammacharoen, Chuchaat; Kongyou, Tassimon

    2007-07-01

    Surface contaminants, such as powder and thin film on various solid surfaces, were analyzed by ATR FT-IR microspectroscopy. An ATR accessory consisting of a miniature-Ge IRE with contact area smaller than 50 microm, in diameter was fabricated and employed for a non-destructive characterization. The IRE was pre-aligned and fixed onto a 15x Schwarzschild-Cassegrain infrared objective. Easy maneuvering of the microscope stage enabled an accumulative collection of the contaminant at the tip of a miniature-Ge IRE, where the contaminants were analyzed under the ATR condition. By making a gentle contact between the Ge tip and selected area on the surface, any removable contaminants were transferred onto the Ge tip where its molecular information was acquired without any interference from the solid substrate. A thin organic film (i.e., mineral oil or fluorolube) was coated at the tip of the IRE in order to enhance the collecting efficiency of the removable contaminants.

  7. Confocal Raman microspectroscopy reveals a convergence of the chemical composition in methanogenic archaea from a Siberian permafrost-affected soil.

    PubMed

    Serrano, Paloma; Hermelink, Antje; Lasch, Peter; de Vera, Jean-Pierre; König, Nicole; Burckhardt, Oliver; Wagner, Dirk

    2015-12-01

    Methanogenic archaea are widespread anaerobic microorganisms responsible for the production of biogenic methane. Several new species of psychrotolerant methanogenic archaea were recently isolated from a permafrost-affected soil in the Lena Delta (Siberia, Russia), showing an exceptional resistance against desiccation, osmotic stress, low temperatures, starvation, UV and ionizing radiation when compared to methanogens from non-permafrost environments. To gain a deeper insight into the differences observed in their resistance, we described the chemical composition of methanogenic strains from permafrost and non-permafrost environments using confocal Raman microspectroscopy (CRM). CRM is a powerful tool for microbial identification and provides fingerprint-like information about the chemical composition of the cells. Our results show that the chemical composition of methanogens from permafrost-affected soils presents a high homology and is remarkably different from strains inhabiting non-permafrost environments. In addition, we performed a phylogenetic reconstruction of the studied strains based on the functional gene mcrA to prove the different evolutionary relationship of the permafrost strains. We conclude that the permafrost methanogenic strains show a convergent chemical composition regardless of their genotype. This fact is likely to be the consequence of a complex adaptive process to the Siberian permafrost environment and might be the reason underlying their resistant nature.

  8. Vibrational microspectroscopic identification of powdered traditional medicines: Chemical micromorphology of Poria observed by infrared and Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Jian-bo; Sun, Su-qin; Ma, Fang; Zhou, Qun

    2014-07-01

    Microscopic identification using optical microscopes is a simple and effective method to identify powdered traditional medicines made from plants, animals and fungi. Sometimes, the criteria based on physical properties of the microscopic characteristics of drug powder may be ambiguous, which makes the microscopic identification method subjective and empirical to some extent. In this research, the vibrational microspectroscopic identification method is proposed for more explicit discrimination of powdered traditional medicines. The chemical micromorphology, i.e., chemical compositions and related physical morphologies, of the drug powder can be profiled objectively and quantitatively by infrared and Raman microspectroscopy, leading to better understanding about the formation mechanisms of microscopic characteristics and more accurate identification criteria. As an example, the powder of Poria, which is one of the most used traditional Chinese medicines, is studied in this research. Three types of hyphae are classified according to their infrared spectral features in the region from 1200 to 900 cm-1. Different kinds of polysaccharides indicate that these hyphae may be in different stages of the growth. The granular and branched clumps observed by the optical microscope may be formed from the aggregation of the mature hyphae with β-D-glucan reserves. The newfound spherical particles may originate from the exuded droplets in the fresh Poria because they are both composed of α-D-glucan. The results are helpful to understand the development of the hyphae and the formation of active polysaccharides in Poria and to establish accurate microspectroscopic identification criteria.

  9. Single Cell Synchrotron FT-IR Microspectroscopy Reveals a Link between Neutral Lipid and Storage Carbohydrate Fluxes in S. cerevisiae

    PubMed Central

    Jamme, Frédéric; Vindigni, Jean-David; Méchin, Valérie; Cherifi, Tamazight; Chardot, Thierry; Froissard, Marine

    2013-01-01

    In most organisms, storage lipids are packaged into specialized structures called lipid droplets. These contain a core of neutral lipids surrounded by a monolayer of phospholipids, and various proteins which vary depending on the species. Hydrophobic structural proteins stabilize the interface between the lipid core and aqueous cellular environment (perilipin family of proteins, apolipoproteins, oleosins). We developed a genetic approach using heterologous expression in Saccharomyces cerevisiae of the Arabidopsis thaliana lipid droplet oleosin and caleosin proteins AtOle1 and AtClo1. These transformed yeasts overaccumulate lipid droplets, leading to a specific increase in storage lipids. The phenotype of these cells was explored using synchrotron FT-IR microspectroscopy to investigate the dynamics of lipid storage and cellular carbon fluxes reflected as changes in spectral fingerprints. Multivariate statistical analysis of the data showed a clear effect on storage carbohydrates and more specifically, a decrease in glycogen in our modified strains. These observations were confirmed by biochemical quantification of the storage carbohydrates glycogen and trehalose. Our results demonstrate that neutral lipid and storage carbohydrate fluxes are tightly connected and co-regulated. PMID:24040242

  10. Synchrotron-FTIR microspectroscopy enables the distinction of lipid accumulation in thraustochytrid strains through analysis of individual live cells.

    PubMed

    Vongsvivut, Jitraporn; Heraud, Philip; Gupta, Adarsha; Thyagarajan, Tamilselvi; Puri, Munish; McNaughton, Don; Barrow, Colin J

    2015-02-01

    The superior characteristics of high photon flux and diffraction-limited spatial resolution achieved by synchrotron-FTIR microspectroscopy allowed molecular characterization of individual live thraustochytrids. Principal component analysis revealed distinct separation of the single live cell spectra into their corresponding strains, comprised of new Australasian thraustochytrids (AMCQS5-5 and S7) and standard cultures (AH-2 and S31). Unsupervised hierarchical cluster analysis (UHCA) indicated close similarities between S7 and AH-7 strains, with AMCQS5-5 being distinctly different. UHCA correlation conformed well to the fatty acid profiles, indicating the type of fatty acids as a critical factor in chemotaxonomic discrimination of these thraustochytrids and also revealing the distinctively high polyunsaturated fatty acid content as key identity of AMCQS5-5. Partial least squares discriminant analysis using cross-validation approach between two replicate datasets was demonstrated to be a powerful classification method leading to models of high robustness and 100% predictive accuracy for strain identification. The results emphasized the exceptional S-FTIR capability to perform real-time in vivo measurement of single live cells directly within their original medium, providing unique information on cell variability among the population of each isolate and evidence of spontaneous lipid peroxidation that could lead to deeper understanding of lipid production and oxidation in thraustochytrids for single-cell oil development. Copyright © 2014 Elsevier GmbH. All rights reserved.

  11. Subcellular Raman Microspectroscopy Imaging of Nucleic Acids and Tryptophan for Distinction of Normal Human Skin Cells and Tumorigenic Keratinocytes.

    PubMed

    Piredda, Paola; Berning, Manuel; Boukamp, Petra; Volkmer, Andreas

    2015-07-07

    At present, tumor diagnostic imaging is commonly based on hematoxylin and eosin or immunohistochemical staining of biopsies, which requires tissue excision, fixation, and staining with exogenous marker molecules. Here, we report on label-free tumor imaging using confocal spontaneous Raman scattering microspectroscopy, which exploits the intrinsic vibrational contrast of endogenous biomolecular species. We present a chemically specific and quantitative approach to monitoring normal human skin cells (keratinocytes and fibroblasts) as well as the human HaCaT in vitro skin carcinogenesis model and the tumor-derived MET in vivo skin cancer progression model. Mapping the amplitudes of two spectrally well isolated Raman bands at 752 and 785 cm(-1) allowed for direct visualization of the distributions representative of tryptophan-rich proteins and nucleic acids, respectively, with subcellular spatial resolution. Using these Raman markers, it was feasible to discriminate between normal human epidermal keratinocytes (NHEK) and dermal fibroblasts (NHDF) and to confine all tumorigenic cells from both the NHEK and NHDF. First evidence for the successful application of the proposed intracellular nucleic acid and tryptophan Raman signatures for skin cancer diagnosis was further demonstrated in an organotypic cutaneous squamous cell carcinomas model, allowing for the identification of tumor cells and their surrounding stroma in the tissue context.

  12. The Use of Synchrotron Infrared Microspectroscopy in the Assessment of Cutaneous T-cell Lymphoma vs. Pityriasis lichenoides Chronica

    SciTech Connect

    El Bedewi, A.; El Anany, G; El Mofty, M; Kretlow, A; Park, S; Miller, L

    2010-01-01

    The diagnosis of cutaneous lymphomas remains a challenge for both the clinician and dermatopathologist. To differentiate between frank malignant and premalignant lymphocytes within the skin. This study was performed on 20 patients with a mean age of 50 years. They were divided into two groups: mycosis fungoides (MF) (stage IA, IB and IIA) and pityriasis lichenoides chronica (PLC). Immunophenotyping using antibodies CD3, CD4, CD8, CD20 and CD30 was performed. Synchrotron Fourier transform infrared microspectroscopy (S-FTIRM) was performed on cell nuclei to assess chemical differences between MF and PLC cases as a potential complementary screening tool. Dermal spectra of both MF and PLC were compared using principal components analysis (PCA) of the S-FTIRM data. All PLC spectra was clustered together. However, the MF spectra formed two clusters, one that grouped with the PLC and the other grouped separately. Moreover, protein and nucleic acids showed highly significant differences between MF (IIA and IB), MF (IA) and PLC. The malignant transformation within lymphocytes was identifiable through the spectroscopic analysis of protein, RNA and DNA with S-FTIRM, making it a promising tool for classifying the progression of cutaneous T-cell lymphoma.

  13. In situ observation of dynamic electrodeposition processes by soft x-ray fluorescence microspectroscopy and keyhole coherent diffractive imaging

    NASA Astrophysics Data System (ADS)

    Bozzini, Benedetto; Kourousias, George; Gianoncelli, Alessandra

    2017-03-01

    This paper describes two novel in situ microspectroscopic approaches to the dynamic study of electrodeposition processes: x-ray fluorescence (XRF) mapping with submicrometric space resolution and keyhole coherent diffractive imaging (kCDI) with nanometric lateral resolution. As a case study, we consider the pulse-plating of nanocomposites with polypyrrole matrix and Mn x Co y O z dispersoids, a prospective cathode material for zinc-air batteries. This study is centred on the detailed measurement of the elemental distributions developing in two representative subsequent growth steps, based on the combination of in situ identical-location XRF microspectroscopy—accompanied by soft-x ray absorption microscopy—and kCDI. XRF discloses space and time distributions of the two electrodeposited metals and kCDI on the one hand allows nanometric resolution and on the other hand provides complementary absorption as well as phase contrast modes. The joint information derived from these two microspectroscopies allows measurement of otherwise inaccessible observables that are a prerequisite for electrodeposition modelling and control accounting for dynamic localization processes.

  14. Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time

    PubMed Central

    Hall, Edward K; Singer, Gabriel A; Pölzl, Marvin; Hämmerle, Ieda; Schwarz, Christian; Daims, Holger; Maixner, Frank; Battin, Tom J

    2011-01-01

    Stoichiometry of microbial biomass is a key determinant of nutrient recycling in a wide variety of ecosystems. However, little is known about the underlying causes of variance in microbial biomass stoichiometry. This is primarily because of technological constraints limiting the analysis of macromolecular composition to large quantities of microbial biomass. Here, we use Raman microspectroscopy (MS), to analyze the macromolecular composition of single cells of two species of bacteria grown on minimal media over a wide range of resource stoichiometry. We show that macromolecular composition, determined from a subset of identified peaks within the Raman spectra, was consistent with macromolecular composition determined using traditional analytical methods. In addition, macromolecular composition determined by Raman MS correlated with total biomass stoichiometry, indicating that analysis with Raman MS included a large proportion of a cell's total macromolecular composition. Growth phase (logarithmic or stationary), resource stoichiometry and species identity each influenced each organism's macromolecular composition and thus biomass stoichiometry. Interestingly, the least variable peaks in the Raman spectra were those responsible for differentiation between species, suggesting a phylogenetically specific cellular architecture. As Raman MS has been previously shown to be applicable to cells sampled directly from complex environments, our results suggest Raman MS is an extremely useful application for evaluating the biomass stoichiometry of environmental microorganisms. This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity. PMID:20703314

  15. In-vitro analysis of normal and aneurismal human ascending aortic tissues using FT-IR microspectroscopy.

    PubMed

    Bonnier, F; Rubin, S; Ventéo, L; Krishna, C M; Pluot, M; Baehrel, B; Manfait, M; Sockalingum, G D

    2006-07-01

    FTIR microspectroscopy has shown to be a proven tool in the investigation of many tissue types. We have used this spectroscopic approach to analyse structural differences between normal and aneurismal aortic tissues and also aortas from patients with congenital anomalies like aortic bicuspid valves. Spectral analysis showed important variations in amide I and II regions, related to changes in alpha-helix and beta-sheet secondary structure of proteins that seem to be correlated to structural modifications of collagen and elastin. These proteins are the major constituents of the aortic wall associated to smooth muscular cells. The amide regions have thus been identified as a marker of structural modifications related to these proteins whose modifications can be associated to a given aortic pathological situation. Both univariate (total absorbance image and band ratio) and multivariate (principal components analysis) analyses of the spectral information contained in the infrared images have been performed. Differences between tissues have been identified by these two approaches and allowed to separate each group of aortic tissues. However, with univariate band ratio analysis, the pathological group was found to be composed of samples from aneurismal aortas associated or not with an aortic bicuspid valve. In contrast, PCA was able to separate these two types of aortic pathologies. For other groups, PCA and band ratio analysis can differentiate between normal, aneurismal, and none dilated aortas from patients with a bicuspid aortic valve.

  16. A new approach to studying the effects of ionising radiation on single cells using FTIR synchrotron microspectroscopy

    NASA Astrophysics Data System (ADS)

    Lipiec, E.; Birarda, G.; Kowalska, J.; Lekki, J.; Vaccari, L.; Wiecheć, A.; Wood, B. R.; Kwiatek, W. M.

    2013-12-01

    The effect of ionizing radiation on single cells using a proton source was investigated using Fourier transform infrared (FTIR) microspectroscopy. The prostate cancer cells (DU-145) were irradiated by a specific number (50, 200, 400, 2000 and 4000) of protons per cell. Next after fixing the cells with 70% ethanol micro-FTIR spectra were obtained using both: (a) the synchrotron radiation source with a Mercury-Cadmium-Telluride (MCT) detector and (b) a globar source with a focal plane array (FPA) detector. FTIR spectra obtained from both instrumental configurations were analyzed independently to investigate the changes in the DNA phosphodiester region (1150-950 cm-1) of irradiated and control (untreated by ionizing radiation) cells. A Principal Component Analysis (PCA) scores plot revealed distinct clusters for all groups of irradiated cells, even for those irradiated by the smallest dose of protons. The dose-dependent changes in the relative intensities of DNA peak at 970 cm-1 (ribose-phosphate skeletal motions), along with a shift of the O-P-O band corresponding to the symmetric phosphodiester stretching mode at 1090 cm-1 were observed. The results demonstrate that FTIR spectroscopy is a promising tool to investigate DNA damage in single cells and may become an important tool in assessing cell damage following radiotherapy.

  17. Transmission Fourier transform infrared microspectroscopy allows simultaneous assessment of cutin and cell-wall polysaccharides of Arabidopsis petals.

    PubMed

    Mazurek, Sylwester; Mucciolo, Antonio; Humbel, Bruno M; Nawrath, Christiane

    2013-06-01

    A procedure for the simultaneous analysis of cell-wall polysaccharides, amides and aliphatic polyesters by transmission Fourier transform infrared microspectroscopy (FTIR) has been established for Arabidopsis petals. The combination of FTIR imaging with spectra derivatization revealed that petals, in contrast to other organs, have a characteristic chemical zoning with high amount of aliphatic compounds and esters in the lamina and of polysaccharides in the stalk of the petal. The hinge region of petals was particular rich in amides as well as in vibrations potentially associated with hemicellulose. In addition, a number of other distribution patterns have been identified. Analyses of mutants in cutin deposition confirmed that vibrations of aliphatic compounds and esters present in the lamina were largely associated with the cuticular polyester. Calculation of spectrotypes, including the standard deviation of intensities, allowed detailed comparison of the spectral features of various mutants. The spectrotypes not only revealed differences in the amount of polyesters in cutin mutants, but also changes in other compound classes. For example, in addition to the expected strong deficiencies in polyester content, the long-chain acyl CoA synthase 2 mutant showed increased intensities of vibrations in a wavelength range that is typical for polysaccharides. Identical spectral features were observed in quasimodo2, a cell-wall mutant of Arabidopsis with a defect in pectin formation that exhibits increased cellulose synthase activity. FTIR thus proved to be a convenient method for the identification and characterization of mutants affected in the deposition of cutin in petals.

  18. High spatial resolution infrared micro-spectroscopy reveals the mechanism of leaf lignin decomposition by aquatic fungi.

    PubMed

    Kerr, Janice L; Baldwin, Darren S; Tobin, Mark J; Puskar, Ljiljana; Kappen, Peter; Rees, Gavin N; Silvester, Ewen

    2013-01-01

    Organic carbon is a critical component of aquatic systems, providing energy storage and transfer between organisms. Fungi are a major decomposer group in the aquatic carbon cycle, and are one of few groups thought to be capable of breaking down woody (lignified) tissue. In this work we have used high spatial resolution (synchrotron light source) infrared micro-spectroscopy to study the interaction between aquatic fungi and lignified leaf vein material (xylem) from River Redgum trees (E. camaldulensis) endemic to the lowland rivers of South-Eastern Australia. The work provides spatially explicit evidence that fungal colonisation of leaf litter involves the oxidative breakdown of lignin immediately adjacent to the fungal tissue and depletion of the lignin-bound cellulose. Cellulose depletion occurs over relatively short length scales (5-15 µm) and highlights the likely importance of mechanical breakdown in accessing the carbohydrate content of this resource. Low bioavailability compounds (oxidized lignin and polyphenols of plant origin) remain in colonised leaves, even after fungal activity diminishes, and suggests a possible pathway for the sequestration of carbon in wetlands. The work shows that fungi likely have a critical role in the partitioning of lignified material into a biodegradable fraction that can re-enter the aquatic carbon cycle, and a recalcitrant fraction that enters long-term storage in sediments or contribute to the formation of dissolved organic carbon in the water column.

  19. Two refractory Wild 2 terminal particles from a carrot-shaped track characterized combining MIR/FIR/Raman microspectroscopy and FE-SEM/EDS analyses

    NASA Astrophysics Data System (ADS)

    Rotundi, A.; Rietmeijer, F. J. M.; Ferrari, M.; Della Corte, V.; Baratta, G. A.; Brunetto, R.; Dartois, E.; Djouadi, Z.; Merouane, S.; Borg, J.; Brucato, J. R.; Sergeant D'Hendecourt, L.; Mennella, V.; Palumbo, M. E.; Palumbo, P.

    2014-04-01

    We present the analyses results of two bulk Terminal Particles, C2112,7,171,0,0 and C2112,9,171,0,0, derived from the Jupiter-family comet 81P/Wild 2 returned by the Stardust mission. Each particle embedded in a slab of silica aerogel was pressed in a diamond cell. This preparation, as expected, made it difficult to identify the minerals and organic materials present in these particles. This problem was overcome using a combination of three different analytical techniques, viz. FE-SEM/EDS, IR, and Raman microspectroscopy that allowed identifying the minerals and small amounts of amorphous carbon present in both particles. TP2 and TP3 were dominated by Ca-free and low-Ca, Mg-rich, Mg,Fe-olivine. The presence of melilite in both particles is supported by IR microspectroscopy, but is not confirmed by Raman microspectroscopy, possibly because the amounts are too small to be detected. TP2 and TP3 show similar silicate mineral compositions, but Ni-free and low-Ni, subsulfur (Fe,Ni)S grains are present in TP2 only. TP2 contains indigenous amorphous carbon hot spots; no indigenous carbon was identified in TP3. These nonchondritic particles probably originated in a differentiated body. This work found an unanticipated carbon contamination following the FE-SEM/EDS analyses. It is suggested that organic materials in the embedding silica aerogel are irradiated during FE-SEM/EDS analyses creating a carbon gas that develops a strong fluorescence continuum. The combination of the selected analytical techniques can be used to characterize bulk Wild 2 particles without the need of extraction and removal of the encapsulating aerogel. This approach offers a relatively fast sample preparation procedure, but compressing the samples can cause spurious artifacts, viz. silica contamination. Because of the combination of techniques, we account for these artifacts.

  20. A method to obtain the absorption coefficient spectrum of single grain coal in the aliphatic C-H stretching region using infrared transflection microspectroscopy.

    PubMed

    Tonoue, Ryota; Katsura, Makoto; Hamamoto, Mai; Bessho, Hiroki; Nakashima, Satoru

    2014-01-01

    A method was developed to obtain the absorption coefficient spectrum of a grain of coal (as small as 10(-7)) in the region of aliphatic and aromatic C-H stretching bands (2700-3200 cm(-1)) using infrared transflection microspectroscopy. In this method, the complex refractive index n - ik was determined using an optimization algorithm with the Kramers-Kronig transform so that the calculated transflection spectrum from the Fresnel equation corresponded to the measured one. The obtained absorption coefficients were compared with the bulk values determined from the potassium bromide (KBr) pellet measurement method.

  1. Dynamical study of the water penetration process into a cellulose acetate film studied by coherent anti-Stokes Raman scattering (CARS) microspectroscopy

    NASA Astrophysics Data System (ADS)

    Fujisawa, Rie; Ohno, Tomoya; Kaneyasu, Junya F.; Leproux, Philippe; Couderc, Vincent; Kita, Hiroshi; Kano, Hideaki

    2016-07-01

    The penetration process of water into a cellulose acetate film was traced in real time by coherent anti-Stokes Raman scattering (CARS) microspectroscopy. The Cdbnd O stretch mode was red-shifted due to hydrogen-bond formation. We also found that two Raman bands at 1605 cm-1 and 1665 cm-1 emerged only in the early stage of the water penetration process. Based on the combined analysis of the experimental and computational studies, these bands at 1605 cm-1 and 1665 cm-1 were assigned as the OH bend mode due to hydrogen-bonded penetrated water and hydrogen-bonded OH groups in pyranose rings, respectively.

  2. Shielding NSLS-II light source: Importance of geometry for calculating radiation levels from beam losses [Shielding Synchrotron Light Sources: Importance of geometry for calculating radiation levels from beam losses

    SciTech Connect

    Kramer, S. L.; Ghosh, V. J.; Breitfeller, M.; Wahl, W.

    2016-08-10

    Third generation high brightness light sources are designed to have low emittance and high current beams, which contribute to higher beam loss rates that will be compensated by Top-Off injection. Shielding for these higher loss rates will be critical to protect the projected higher occupancy factors for the users. Top-Off injection requires a full energy injector, which will demand greater consideration of the potential abnormal beam miss-steering and localized losses that could occur. The high energy electron injection beam produces significantly higher neutron component dose to the experimental floor than a lower energy beam injection and ramped operations. Minimizing this dose will require adequate knowledge of where the miss-steered beam can occur and sufficient EM shielding close to the loss point, in order to attenuate the energy of the particles in the EM shower below the neutron production threshold (<10 MeV), which will spread the incident energy on the bulk shield walls and thereby the dose penetrating the shield walls. Designing supplemental shielding near the loss point using the analytic shielding model is shown to be inadequate because of its lack of geometry specification for the EM shower process. To predict the dose rates outside the tunnel requires detailed description of the geometry and materials that the beam losses will encounter inside the tunnel. Modern radiation shielding Monte-Carlo codes, like FLUKA, can handle this geometric description of the radiation transport process in sufficient detail, allowing accurate predictions of the dose rates expected and the ability to show weaknesses in the design before a high radiation incident occurs. The effort required to adequately define the accelerator geometry for these codes has been greatly reduced with the implementation of the graphical interface of FLAIR to FLUKA. This made the effective shielding process for NSLS-II quite accurate and reliable. Lastly, the principles used to provide

  3. Vibrational microspectroscopic identification of powdered traditional medicines: chemical micromorphology of Poria observed by infrared and Raman microspectroscopy.

    PubMed

    Chen, Jian-bo; Sun, Su-qin; Ma, Fang; Zhou, Qun

    2014-07-15

    Microscopic identification using optical microscopes is a simple and effective method to identify powdered traditional medicines made from plants, animals and fungi. Sometimes, the criteria based on physical properties of the microscopic characteristics of drug powder may be ambiguous, which makes the microscopic identification method subjective and empirical to some extent. In this research, the vibrational microspectroscopic identification method is proposed for more explicit discrimination of powdered traditional medicines. The chemical micromorphology, i.e., chemical compositions and related physical morphologies, of the drug powder can be profiled objectively and quantitatively by infrared and Raman microspectroscopy, leading to better understanding about the formation mechanisms of microscopic characteristics and more accurate identification criteria. As an example, the powder of Poria, which is one of the most used traditional Chinese medicines, is studied in this research. Three types of hyphae are classified according to their infrared spectral features in the region from 1200 to 900 cm(-1). Different kinds of polysaccharides indicate that these hyphae may be in different stages of the growth. The granular and branched clumps observed by the optical microscope may be formed from the aggregation of the mature hyphae with β-D-glucan reserves. The newfound spherical particles may originate from the exuded droplets in the fresh Poria because they are both composed of α-D-glucan. The results are helpful to understand the development of the hyphae and the formation of active polysaccharides in Poria and to establish accurate microspectroscopic identification criteria. Copyright © 2014 Elsevier B.V. All rights reserved.

  4. Fourier transform infrared microspectroscopy monitoring of 5-fluorouracil-induced apoptosis in SW620 colon cancer cells

    PubMed Central

    GAO, YANFENG; HUO, XIONGWEI; DONG, LIU; SUN, XUEJUN; SAI, HE; WEI, GUANGBING; XU, YIZHUANG; ZHANG, YUANFU; WU, JINGUANG

    2015-01-01

    Colon cancer is associated with a high incidence and a poor prognosis. The aim of the present study was to determine whether Fourier transform infrared (FTIR) microspectroscopy can be used to monitor the chemotherapy drug-induced apoptosis of SW620 colon cancer cells. The 50% inhibitory concentration (IC50) of 5-fluorouracil (5-FU), the main chemotherapeutic agent used for the treatment of colorectal cancer, was determined as the inhibition of growth of the SW620 cells using an MTT assay. Cell starvation and 5-FU treatment synergized to arrest the cells in the G1 and S phases of the cell cycle. FTIR combined with fluorescence activated cell sorting (FACS) analysis were used to analyze the SW620 cells following treatment with 5-FU for 12, 24 and 48 h. The apoptotic cells had several spectral characteristics. The relative peak intensity ratio (I1740/I1460) was significantly increased (P<0.05), the I1740/I1460 ratio, associated with a band of amino acid residues at 1,410 cm−1 was significantly increased at the early and late phases of cell death (P<0.05), the peaks at 1,240 cm−1 increased in wave number, a band at 1,040 cm−1, associated with polysaccharides, appeared at 24 and 48 h and then moved to a higher wave number and the I1040/I1460 ratio increased at the late stage of apoptosis. These results demonstrated that FTIR can be used as a label-free technique to monitor cancer cell apoptosis and to understand the spectral fingerprints of apoptotic cells. This suggested that FTIR spectral features have potential as a powerful tool to monitor cancer cell apoptosis. PMID:25503826

  5. Label-free imaging and identification of typical cells of acute myeloid leukaemia and myelodysplastic syndrome by Raman microspectroscopy.

    PubMed

    Vanna, R; Ronchi, P; Lenferink, A T M; Tresoldi, C; Morasso, C; Mehn, D; Bedoni, M; Picciolini, S; Terstappen, L W M M; Ciceri, F; Otto, C; Gramatica, F

    2015-02-21

    In clinical practice, the diagnosis and classification of acute myeloid leukaemia (AML) and myelodysplastic syndrome (MDS) start from the manual examination of stained smears of bone marrow (BM) and peripheral blood (PB) by using an optical microscope. This step is subjective and scarcely reproducible. Therefore, the development of subjective and potentially automatable methods for the recognition of typical AML/MDS cells is necessary. Here we have used Raman spectroscopy for distinguishing myeloblasts, promyelocytes, abnormal promyelocytes and erhytroblasts, which have to be counted for a correct diagnosis and morphological classification of AML and MDS. BM samples from patients affected by four different AML subtypes, mostly characterized by the presence of the four subpopulations selected for this study, were analyzed. First, each cell was scanned by acquiring 4096 spectra, thus obtaining Raman images which demonstrate an accurate description of morphological features characteristic of each subpopulation. Raman imaging coupled with hierarchical cluster analysis permitted the automatic discrimination and localization of the nucleus, the cytoplasm, myeloperoxidase containing granules and haemoglobin. Second, the averaged Raman fingerprint of each cell was analysed by multivariate analysis (principal component analysis and linear discriminant analysis) in order to study the typical vibrational features of each subpopulation and also for the automatic recognition of cells. The leave-one-out cross validation of a Raman-based classification model demonstrated the correct classification of myeloblasts, promyelocytes (normal/abnormal) and erhytroblasts with an accuracy of 100%. Normal and abnormal promyelocytes were distinguished with 95% accuracy. The overall classification accuracy considering the four subpopulations was 98%. This proof-of-concept study shows that Raman micro-spectroscopy could be a valid approach for developing label-free, objective and automatic

  6. Rapid recognition of drug-resistance/sensitivity in leukemic cells by Fourier transform infrared microspectroscopy and unsupervised hierarchical cluster analysis.

    PubMed

    Bellisola, Giuseppe; Cinque, Gianfelice; Vezzalini, Marzia; Moratti, Elisabetta; Silvestri, Giovannino; Redaelli, Sara; Gambacorti Passerini, Carlo; Wehbe, Katia; Sorio, Claudio

    2013-07-21

    We tested the ability of Fourier Transform (FT) InfraRed (IR) microspectroscopy (microFTIR) in combination with unsupervised Hierarchical Cluster Analysis (HCA) in identifying drug-resistance/sensitivity in leukemic cells exposed to tyrosine kinase inhibitors (TKIs). Experiments were carried out in a well-established mouse model of human Chronic Myelogenous Leukemia (CML). Mouse-derived pro-B Ba/F3 cells transfected with and stably expressing the human p210(BCR-ABL) drug-sensitive wild-type BCR-ABL or the V299L or T315I p210(BCR-ABL) drug-resistant BCR-ABL mutants were exposed to imatinib-mesylate (IMA) or dasatinib (DAS). MicroFTIR was carried out at the Diamond IR beamline MIRIAM where the mid-IR absorbance spectra of individual Ba/F3 cells were acquired using the high brilliance IR synchrotron radiation (SR) via aperture of 15 × 15 μm(2) in sizes. A conventional IR source (globar) was used to compare average spectra over 15 cells or more. IR signatures of drug actions were identified by supervised analyses in the spectra of TKI-sensitive cells. Unsupervised HCA applied to selected intervals of wavenumber allowed us to classify the IR patterns of viable (drug-resistant) and apoptotic (drug-sensitive) cells with an accuracy of >95%. The results from microFTIR + HCA analysis were cross-validated with those obtained via immunochemical methods, i.e. immunoblotting and flow cytometry (FC) that resulted directly and significantly correlated. We conclude that this combined microFTIR + HCA method potentially represents a rapid, convenient and robust screening approach to study the impact of drugs in leukemic cells as well as in peripheral blasts from patients in clinical trials with new anti-leukemic drugs.

  7. In vivo microspectroscopy monitoring of chromium effects on the photosynthetic and photoreceptive apparatus of Eudorina unicocca and Chlorella kessleri.

    PubMed

    Juarez, Angela Beatriz; Barsanti, Laura; Passarelli, Vincenzo; Evangelista, Valter; Vesentini, Nicoletta; Conforti, Visitacion; Gualtieri, Paolo

    2008-11-01

    In microorganisms and plants, chromium (Cr) is not essential for any metabolic process, and can ultimately prove highly deleterious. Due to its widespread industrial use, chromium has become a serious pollutant in diverse environmental settings. The presence of Cr leads to the selection of specific algal populations able to tolerate high levels of Cr compounds. The varying Cr-resistance mechanisms displayed by microorganisms include biosorption, diminished accumulation, precipitation, reduction of Cr(6+) to Cr(3+), and chromate efflux. In this paper we describe the effects of Cr(6+) (the most toxic species) on the photosynthetic and photoreceptive apparatus of two fresh water microalgae, Eudorina unicocca and Chlorella kessleri. We measured the effect of this heavy metal by means of in vivo absorption microspectroscopy of both the thylakoid compartments and the eyespot. The decomposition of the overall absorption spectra in pigment constituents indicates that Cr(6+) effects are very different in the two algae. In E. unicocca the metal induced a complete pheophinitization of the chlorophylls and a modification of the carotenoids present in the eyespot after only 120 h of exposition at a concentration equal or greater than 40 microM, which is the limit for total Cr discharge established by US EPA regulations. In C. kessleri, chromium concentrations a hundred times higher than this limit had no effect on the photosynthetic machinery. The different tolerance level of the two algae is suggested to be due to the different properties of the mucilaginous envelope and cell wall covering, respectively, the colonies of Eudorina and the single cells of Chlorella, which binds chromium cations to a different extent.

  8. On the effect of experimental noise on the classification of biological samples using Raman micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Barton, Sinead J.; Kerr, Laura T.; Domijan, Katarina; Hennelly, Bryan M.

    2016-04-01

    Raman micro-spectroscopy is an optoelectronic technique that can be used to evaluate the chemical composition of biological samples and has been shown to be a powerful diagnostic tool for the investigation of various cancer related diseases including bladder, breast, and cervical cancer. Raman scattering is an inherently weak process with approximately 1 in 107 photons undergoing scattering and for this reason, noise from the recording system can have a significant impact on the quality of the signal, and its suitability for diagnostic classification. The main sources of noise in the recorded signal are shot noise, CCD dark current, and CCD readout noise. Shot noise results from the low signal photon count while dark current results from thermally generated electrons in the semiconductor pixels. Both of these noise sources are time dependent; readout noise is time independent but is inherent in each individual recording and results in the fundamental limit of measurement, arising from the internal electronics of the camera. In this paper, each of the aforementioned noise sources are analysed in isolation, and used to experimentally validate a mathematical model. This model is then used to simulate spectra that might be acquired under various experimental conditions including the use of different cameras, different source wavelength, and power etc. Simulated noisy datasets of T24 and RT112 cell line spectra are generated based on true cell Raman spectrum irradiance values (recorded using very long exposure times) and the addition of simulated noise. These datasets are then input to multivariate classification using Principal Components Analysis and Linear Discriminant Analysis. This method enables an investigation into the effect of noise on the sensitivity and specificity of Raman based classification under various experimental conditions and using different equipment.

  9. Reactivity of Water Soluble Organic Acids with Chloride and Nitrate Particles Investigated by Micro-spectroscopy Analysis

    NASA Astrophysics Data System (ADS)

    Wang, B.; OBrien, R. E.; Kelly, S. T.; Shilling, J. E.; Tivanski, A.; Moffet, R.; Gilles, M. K.; Laskin, A.

    2013-12-01

    Atmospheric particles often consist of a complex organic and inorganic mixture. Interactions between organic and inorganic species may affect particles' chemical and physical properties thus atmospheric chemistry and climate. Water soluble organic acids (WSOA) can contribute a significant fraction of organic materials in condense phase. Inorganic particles, such as sea salt and mineral dust, are main components in the atmosphere and can undergo complex heterogeneous reactions. For example, depletion of chloride in sea salt particles was reported in previous field studies and was attributed to the acid displacement of chlorides with inorganic acids, such as nitric and sulfuric acids. Recently, we showed that NaCl can react with WSOA resulting in the release gaseous HCl and formation of organic salts. A similar mechanism is also applicable to mixed WSOA/nitrate particles where acid displacement reactions are mainly driven by the high volatility and evaporation of HNO3 as particles go through dehydration process. Furthermore, secondary organic material (SOM), which contains a complex mixture of carboxylic acids, exhibits a similar reactivity towards chlorides and nitrates. Here, we present field and laboratory studies on the reactions between atmospheric relevant WSOA/SOM and inorganic salts including NaCl, NaNO3, and Ca(NO3)2 using complementary micro-spectroscopy analysis such as computer controlled scanning electron microscopy with energy dispersive analysis of X-rays (CCSEM/EDX), scanning transmission X-ray microscopy with near edge X-ray absorption fine structure spectroscopy (STXM/NEXAFS), and micro-Fourier transform infrared spectroscopy (micro-FTIR). The results show various potentials of chloride and nitrate depletion by WSOA and SOM. Formation of corresponding organic salts is confirmed and quantified.

  10. Label-free determination of the cell cycle phase in human embryonic stem cells by Raman microspectroscopy.

    PubMed

    Konorov, Stanislav O; Schulze, H Georg; Piret, James M; Blades, Michael W; Turner, Robin F B

    2013-10-01

    The cell cycle is a series of integrated and coordinated physiological events that results in cell growth and replication. Besides observing the event of cell division it is not feasible to determine the cell cycle phase without fatal and/or perturbing invasive procedures such as cell staining, fixing, and/or dissociation. Raman microspectroscopy (RMS) is a chemical imaging technique that exploits molecular vibrations as a contrast mechanism; it can be applied to single living cells noninvasively to allow unperturbed analysis over time. We used RMS to determine the cell cycle phase based on integrating the composite 783 cm(-1) nucleic acid band intensities across individual cell nuclei. After correcting for RNA contributions using the RNA 811 cm(-1) band, the measured intensities essentially reflected DNA content. When quantifying Raman images from single cells in a population of methanol-fixed human embryonic stem cells, the histogram of corrected 783 cm(-1) band intensities exhibited a profile analogous to that obtained using flow-cytometry with nuclear stains. The two population peaks in the histogram occur at Raman intensities corresponding to a 1-fold and 2-fold diploid DNA complement per cell, consistent with a distribution of cells with a population peak due to cells at the end of G1 phase (1-fold) and a peak due to cells entering M phase (2-fold). When treated with EdU to label the replicating DNA and block cell division, cells with higher EdU-related fluorescence generally had higher integrated Raman intensities. This provides proof-of-principle of an analytical method for label-free RMS determination in situ of cell cycle phase in adherent monolayers or even single adherent cells.

  11. Using synchrotron radiation-based infrared microspectroscopy to reveal microchemical structure characterization: frost damaged wheat vs. normal wheat.

    PubMed

    Xin, Hangshu; Zhang, Xuewei; Yu, Peiqiang

    2013-08-14

    This study was conducted to compare: (1) protein chemical characteristics, including the amide I and II region, as well as protein secondary structure; and (2) carbohydrate internal structure and functional groups spectral intensities between the frost damaged wheat and normal wheat using synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIRM). Fingerprint regions of specific interest in our study involved protein and carbohydrate functional group band assignments, including protein amide I and II (ca. 1774-1475 cm(-1)), structural carbohydrates (SCHO, ca. 1498-1176 cm(-1)), cellulosic compounds (CELC, ca. 1295-1176 cm(-1)), total carbohydrates (CHO, ca. 1191-906 cm(-1)) and non-structural carbohydrates (NSCHO, ca. 954-809 cm(-1)). The results showed that frost did cause variations in spectral profiles in wheat grains. Compared with healthy wheat grains, frost damaged wheat had significantly lower (p < 0.05) spectral intensities in height and area ratios of amide I to II and almost all the spectral parameters of carbohydrate-related functional groups, including SCHO, CHO and NSCHO. Furthermore, the height ratio of protein amide I to the third peak of CHO and the area ratios of protein amide (amide I + II) to carbohydrate compounds (CHO and SCHO) were also changed (p < 0.05) in damaged wheat grains. It was concluded that the SR-FTIR microspectroscopic technique was able to examine inherent molecular structure features at an ultra-spatial resolution (10 × 10 μm) between different wheat grains samples. The structural characterization of wheat was influenced by climate conditions, such as frost damage, and these structural variations might be a major reason for the decreases in nutritive values, nutrients availability and milling and baking quality in wheat grains.

  12. Metabolic-Activity-Based Assessment of Antimicrobial Effects by D2O-Labeled Single-Cell Raman Microspectroscopy.

    PubMed

    Tao, Yifan; Wang, Yun; Huang, Shi; Zhu, Pengfei; Huang, Wei E; Ling, Junqi; Xu, Jian

    2017-04-04

    To combat the spread of antibiotic resistance, methods that quantitatively assess the metabolism-inhibiting effects of drugs in a rapid and culture-independent manner are urgently needed. Here using four oral bacteria as models, we show that heavy water (D2O)-based single-cell Raman microspectroscopy (D2O-Raman) can probe bacterial response to different drugs using the Raman shift at the C-D (carbon-deuterium vibration) band in 2040 to 2300 cm(-1) as a universal biomarker for metabolic activity at single-bacterial-cell resolution. The "minimum inhibitory concentration based on metabolic activity" (MIC-MA), defined as the minimal dose under which the median ΔC-D-ratio at 8 h of drug exposure is ≤0 and the standard deviation (SD) of the ΔC-D ratio among individual cells is ≤0.005, was proposed to evaluate the metabolism-inhibiting efficacy of drugs. In addition, heterogeneity index of MIC-MA (MIC-MA-HI), defined as SD of C-D ratio among individual cells, quantitatively assesses the among-cell heterogeneity of metabolic activity after drug regimens. When exposed to 1× MIC of sodium fluoride (NaF), 1× MIC of chlorhexidine (CHX), or 60× MIC of ampicillin, the cariogenic oral pathogen Streptococcus mutans UA159 ceased propagation yet remained metabolically highly active. This underscores the advantage of MIC-MA over the growth-based MIC in being able to detect the "nongrowing but metabolically active" (NGMA) cells that underlie many latent or recurring infections. Moreover, antibiotic susceptible and resistant S. mutans strains can be readily discriminated at as early as 0.5 h. Thus, D2O-Raman can serve as a universal method for rapid and quantitative assessment of antimicrobial effects based on general metabolic activity at single-cell resolution.

  13. Using Synchrotron Radiation-Based Infrared Microspectroscopy to Reveal Microchemical Structure Characterization: Frost Damaged Wheat vs. Normal Wheat

    PubMed Central

    Xin, Hangshu; Zhang, Xuewei; Yu, Peiqiang

    2013-01-01

    This study was conducted to compare: (1) protein chemical characteristics, including the amide I and II region, as well as protein secondary structure; and (2) carbohydrate internal structure and functional groups spectral intensities between the frost damaged wheat and normal wheat using synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIRM). Fingerprint regions of specific interest in our study involved protein and carbohydrate functional group band assignments, including protein amide I and II (ca. 1774–1475 cm−1), structural carbohydrates (SCHO, ca. 1498–1176 cm−1), cellulosic compounds (CELC, ca. 1295–1176 cm−1), total carbohydrates (CHO, ca. 1191–906 cm−1) and non-structural carbohydrates (NSCHO, ca. 954–809 cm−1). The results showed that frost did cause variations in spectral profiles in wheat grains. Compared with healthy wheat grains, frost damaged wheat had significantly lower (p < 0.05) spectral intensities in height and area ratios of amide I to II and almost all the spectral parameters of carbohydrate-related functional groups, including SCHO, CHO and NSCHO. Furthermore, the height ratio of protein amide I to the third peak of CHO and the area ratios of protein amide (amide I + II) to carbohydrate compounds (CHO and SCHO) were also changed (p < 0.05) in damaged wheat grains. It was concluded that the SR-FTIR microspectroscopic technique was able to examine inherent molecular structure features at an ultra-spatial resolution (10 × 10 μm) between different wheat grains samples. The structural characterization of wheat was influenced by climate conditions, such as frost damage, and these structural variations might be a major reason for the decreases in nutritive values, nutrients availability and milling and baking quality in wheat grains. PMID:23949633

  14. Towards intra-operative diagnosis of tumours during breast conserving surgery by selective-sampling Raman micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Kong, Kenny; Zaabar, Fazliyana; Rakha, Emad; Ellis, Ian; Koloydenko, Alexey; Notingher, Ioan

    2014-10-01

    Breast-conserving surgery (BCS) is increasingly employed for the treatment of early stage breast cancer. One of the key challenges in BCS is to ensure complete removal of the tumour while conserving as much healthy tissue as possible. In this study we have investigated the potential of Raman micro-spectroscopy (RMS) for automated intra-operative evaluation of tumour excision. First, a multivariate classification model based on Raman spectra of normal and malignant breast tissue samples was built and achieved diagnosis of mammary ductal carcinoma (DC) with 95.6% sensitivity and 96.2% specificity (5-fold cross-validation). The tumour regions were discriminated from the healthy tissue structures based on increased concentration of nucleic acids and reduced concentration of collagen and fat. The multivariate classification model was then applied to sections from fresh tissue of new patients to produce diagnosis images for DC. The diagnosis images obtained by raster scanning RMS were in agreement with the conventional histopathology diagnosis but were limited to long data acquisition times (typically 10 000 spectra mm-2, which is equivalent to ~5 h mm-2). Selective-sampling based on integrated auto-fluorescence imaging and Raman spectroscopy was used to reduce the number of Raman spectra to ~20 spectra mm-2, which is equivalent to an acquisition time of ~15 min for 5 × 5 mm2 tissue samples. This study suggests that selective-sampling Raman microscopy has the potential to provide a rapid and objective intra-operative method to detect mammary carcinoma in tissue and assess resection margins.

  15. Topography, nanomechanics, and cell surface components of cancer cells examined by combined atomic force microscopy and Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Wu, Yangzhe; McEwen, Gerald D.; Baker, Sherry M.; Yu, Tian; Gilbertson, Timothy A.; DeWald, Daryll B.; Zhou, Anhong

    2010-02-01

    The investigation of the nanostructures and hydrophobic properties of cancer cell membranes is of importance for elucidating the plasma membrane roles in protein folding, membrane fusion, and cell adhesion that are directly related to cancer cell biophysical properties, such as aggressive growth and migration. On the other hand, the chemical component analysis of the cancer cell membrane could be potentially applied in the clinical diagnosis of cancer by the identification of specific biomarker receptors expressed on cancer cell surfaces. In the present work, a combined atomic force microscopy (AFM) and Raman microspectroscopy technique was applied to detect the difference in nanomechanics and membrane chemical components between two cancer cell lines, human lung adenocarcinoma epithelial cells (A549) and human breast cancer cells (MDA-MB-435 with and without expression of BRMS1 metastasis suppressor). The membrane surface adhesion forces for these cancer cells acquired in culture medium were measured using AFM at 0.478+/-0.091 nN for A549 cells, 0.253+/-0.070 nN for 435 cells, and 1.114+/-0.281 nN for 435/BRMS1 cells, and the cell spring constant was measured at 2.62+/-0.682 mN/m for A549 cells, 2.105+/-0.691 mN/m for 435 cells, and 5.448+/-1.081 mN/m for 435/BRMS1 cells. Raman spectral analysis indicated similar peaks between the A549 cells and the breast cancer cell lines 435 and 435/BRMS1 including ~720 cm-1 (guanine band of DNA), 940 cm-1 (skeletal mode polysaccharide), 1006 cm-1 (symmetric ring breathing phenylalanine), and 1451 cm-1 (CH deformation). Slight variations were observed between ~780 - 985 cm-1 (DNA/RNA and proteins) and 1035 - 1210 cm-1 (lipid and proteins).

  16. Discrimination between basal cell carcinoma and hair follicles in skin tissue sections by Raman micro-spectroscopy

    NASA Astrophysics Data System (ADS)

    Larraona-Puy, M.; Ghita, A.; Zoladek, A.; Perkins, W.; Varma, S.; Leach, I. H.; Koloydenko, A. A.; Williams, H.; Notingher, I.

    2011-05-01

    Skin cancer is the most common human malignancy and basal cell carcinoma (BCC) represents approximately 80% of the non-melanoma cases. Current methods of treatment require histopathological evaluation of the tissues by qualified personnel. However, this method is subjective and in some cases BCC can be confused with other structures in healthy skin, including hair follicles. In this preliminary study, we investigated the potential of Raman micro-spectroscopy (RMS) to discriminate between hair follicles and BCC in skin tissue sections excised during Mohs micrographic surgery (MMS). Imaging and diagnosis of skin sections was automatically generated using ' a priori'-built spectral model based on LDA. This model had 90 ± 9% sensitivity and 85 ± 9% specificity for discrimination of BCC from dermis and epidermis. The model used selected Raman bands corresponding to the largest spectral differences between the Raman spectra of BCC and the normal skin regions, associated mainly with nucleic acids and collagen type I. Raman spectra corresponding to the epidermis regions of the hair follicles were found to be closer to those of healthy epidermis rather than BCC. Comparison between Raman spectral images and the gold standard haematoxylin and eosin (H&E) histopathology diagnosis showed good agreement. Some hair follicle regions were misclassified as BCC; regions corresponded mainly to the outermost layer of hair follicle (basal cells) which are expected to have higher nucleic acid concentration. This preliminary study shows the ability of RMS to distinguish between BCC and other tissue structures associated to healthy skin which can be confused with BCC due to their similar morphology.

  17. ZrO2 nanoparticles labeled via a native protein corona: detection by fluorescence microscopy and Raman microspectroscopy in rat lungs.

    PubMed

    Silge, Anja; Bräutigam, Katharina; Bocklitz, Thomas; Rösch, Petra; Vennemann, Antje; Schmitz, Inge; Popp, Jürgen; Wiemann, Martin

    2015-08-07

    ZrO2 nanoparticles are frequently used in composite materials such as dental fillers from where they may be released and inhaled upon polishing and grinding. Since the overall distribution of ZrO2 NP inside the lung parenchyma can hardly be observed by routine histology, here a labeling with a fluorphore was used secondary to the adsorption of serum proteins. Particles were then intratracheally instilled into rat lungs. After 3 h fluorescent structures consisted of agglomerates scattered throughout the lung parenchyma, which were mainly concentrated in alveolar macrophages after 3 d. A detection method based on Raman microspectroscopy was established to investigate the chemical composition of those fluorescent structures in detail. Raman measurements were arranged such that no spectral interference with the protein-bound fluorescence label was evident. Applying chemometrical methods, Raman signals of the ZrO2 nanomaterial were co-localized with the fluorescence label, indicating the stability of the nanomaterial-protein-dye complex inside the rat lung. The combination of Raman microspectroscopy and adsorptive fluorescence labeling may, therefore, become a useful tool for studying the localization of protein-coated nanomaterials in cells and tissues.

  18. In vivo confocal Raman microspectroscopy of the human skin: highlighting of spectral markers associated to aging via a research of correlation between Raman and biometric mechanical measurements.

    PubMed

    Eklouh-Molinier, Christophe; Gaydou, Vincent; Froigneux, Emmanuel; Barlier, Pascale; Couturaud, Virginie; Manfait, Michel; Piot, Olivier

    2015-11-01

    Skin plays a protective role against the loss of water and external aggression, including mechanical stresses. These crucial functions are ensured by different cutaneous layers, particularly the stratum corneum (SC). During aging, the human skin reveals some apparent modifications of functionalities such as a loss of elasticity. Our investigations aimed at demonstrating that Raman microspectroscopy, as a label-free technique with a high molecular specificity, is efficient to assess in vivo the molecular composition of the skin and the alterations underwent during aging. Our approach was based on a search for correlation between Raman data collected on healthy female volunteers of different ages (from 21 to 70 years old) by means of a remote confocal Raman and skin firmness measurements used as a reference method. Raman and biometric data were then submitted to a partial least square (PLS)-based data processing. Our experiments demonstrated the potential of Raman microspectroscopy to provide an objective in vivo assessment of the skin "biological age" that can be very different from the "chronological age" of the person. In addition, Raman features sensitive to the elasticity and the fatigability of the SC were highlighted. Thereafter, calibration transfer functions were constructed to show the possibility to compare the results obtained during two distinct measurement campaigns conducted with two Raman probes of the same conception. This approach could lead to several interesting prospects, in particular by objectifying the effects of dermocosmetic products on the superficial layers of the skin and by accessing some underlying molecular mechanisms.

  19. Determination of the sequence of intersecting lines from laser toner and seal ink by Fourier transform infrared microspectroscopy and scanning electron microscope / energy dispersive X-ray mapping.

    PubMed

    Wang, Yuanfeng; Li, Bing

    2012-06-01

    The aim of this study was to verify that the combination of Fourier transform infrared microspectroscopy and scanning electron microscope / energy dispersive X-ray mapping could be applied to line intersection problems. The spectral data of red seal ink, laser toner and their intersections, such as peak location and peak intensity, were described. Relative peak height ratios of different chemical components in intersecting lines were used to distinguish the sequences. Energy dispersive X-ray mapping characteristics of intersecting areas were also detailed. The results show that both the laser toner and the seal ink appear on the surface of intersections, regardless of the sequence. The distribution of the two inks on the surface is influenced not only by the sequence of heterogeneous lines but also by diffusion. Fourier transform infrared microspectroscopy and scanning electron microscope/energy dispersive X-ray mapping are able to explore the chemical components and the corresponding elemental distribution in the intersections. The combination of these two techniques has provided a reliable method for sequencing intersecting lines of red seal ink and laser toner, and more importantly, this method may be a basis for sequencing superimposed lines from other writing instruments.

  20. On source identification and alteration of single diesel and wood smoke soot particles in the atmosphere; an X-ray microspectroscopy study.

    PubMed

    Vernooij, M G C; Mohr, M; Tzvetkov, G; Zelenay, V; Huthwelker, T; Kaegi, R; Gehrig, R; Grobéty, B

    2009-07-15

    Diesel and wood combustion are major sources of carbonaceous particles in the atmosphere. It is very hard to distinguish between the two sources by looking at soot particle morphology, but clear differences in the chemical structure of single particles are revealed by C(1s) NEXAFS (near edge X-ray absorption fine structure) microspectroscopy. Soot from diesel combustion has a dominant spectral signature at approximately 285 eV from aromatic pi-bonds, whereas soot from wood combustion has the strongest signature at approximately 287 eV from phenolic carbon bonds. To investigate if it is possible to use these signatures for source apportionment purposes, we collected atmospheric samples with either diesel or wood combustion as a dominant particle source. No spectra obtained from the atmospheric particles completely matched the emission spectra. Especially particles from the wood dominated location underwent large modifications; the phenolic spectral signature at approximately 287 eV is greatly suppressed and surpassed by the peak attributed to the aromatic carbon groups at approximately 285 eV. Comparison with spectra from diesel soot samples experimentally aged with ozone show that very fast modification of the carbon structure of soot particles occurs as soon as they enter the atmosphere. Source attribution of single soot particles with microspectroscopy is thus hardly possible, but NEXAFS remains a powerful tool to study aging effects.

  1. Cell-specific chemotyping and multivariate imaging by combined FT-IR microspectroscopy and orthogonal projections to latent structures (OPLS) analysis reveals the chemical landscape of secondary xylem.

    PubMed

    Gorzsás, András; Stenlund, Hans; Persson, Per; Trygg, Johan; Sundberg, Björn

    2011-06-01

    Fourier-transform infrared (FT-IR) spectroscopy combined with microscopy enables chemical information to be acquired from native plant cell walls with high spatial resolution. Combined with a 64 × 64 focal plane array (FPA) detector, 4096 spectra can be simultaneously obtained from a 0.3 × 0.3 mm image; each spectrum represents a compositional and structural 'fingerprint' of all cell wall components. For optimal use and analysis of such a large amount of information, multivariate approaches are preferred. Here, FT-IR microspectroscopy with FPA detection is combined with orthogonal projections to latent structures discriminant analysis (OPLS-DA). This allows for: (i) the extraction of spectra from single cell types, (ii) identification and characterization of different chemotypes using the full spectral information, and (iii) further visualization of the pattern of identified chemotypes by multivariate imaging. As proof of concept, the chemotypes of Populus tremula xylem cell types are described. The approach revealed unknown features about chemical plasticity and patterns of lignin composition in wood fibers that would have remained hidden in the dataset with traditional data analysis. The applicability of the method to Arabidopsis xylem and its usefulness in mutant chemotyping is also demonstrated. The methodological approach is not limited to xylem tissues but can be applied to any plant organ/tissue also using other techniques such as Raman and UV microspectroscopy.

  2. Partial least squares regression and fourier transform infrared (FTIR) microspectroscopy for prediction of resistance in hepatocellular carcinoma HepG2 cells.

    PubMed

    Junhom, Cholpajsorn; Weerapreeyakul, Natthida; Tanthanuch, Waraporn; Thumanu, Kanjana

    2017-02-01

    We evaluated the feasibility of FTIR microspectroscopy combined with partial least squares regression (PLS-R) for determination of resistance in HepG2 cells. Cell viability testing was performed using neutral red assay for the concentration of cisplatin resulting in 50% antiproliferation (IC50). The resistance index (RI) is the ratio of the IC50 in resistant HepG2 cells vs. parental HepG2 cells. Principal component and unsupervised hierarchical cluster analyses were applied and a differentiation of samples of cells (parental, 1.8RI, 2.3RI, 3.0RI, and 3.5RI) was demonstrated (3000-2800cm(-1) in the lipid and 1700-1500cm(-1) in the protein regions. The FTIR spectra were preprocessed with several treatments to test the algorithm. PLS-R models were built using the 1170 spectra of the HepG2 cells. Cross-validation was used to evaluate prediction of the RI value using this model. PLS-R models-preprocessed with the second derivative FTIR spectra-yielded the best model (R(2)=0.99, RMSEE=0.095 and RPD=7.98). Most RI values were predicted with high accuracy (91-100%) such that the linear correlation between the actual and predicted RI values was nearly perfect (slope~1). FTIR microspectroscopy combined with chemometric analysis using PLS-R offers quick, accurate, and reliable quantitative analysis of HepG2 cell resistance.

  3. Elucidation of adsorption mechanism of bone-staining agent alizarin red S on hydroxyapatite by FT-IR microspectroscopy.

    PubMed

    Moriguchi, T; Yano, K; Nakagawa, S; Kaji, F

    2003-04-01

    To elucidate adsorption mechanism of alizarin red S (ARS), which is often used for staining bones in histology, adsorption of ARS on hydroxyapatite, Ca10(PO4)6(OH)2 (HAP), was investigated by a batch method, compared with alizarin, phenols, and benzenesulfonates. We found that ionized 1-, 2-OH groups (1-, 2-O(-)) of ARS can be electrostatically bound to Ca2+ on HAP, but that the 3-SO3(-) group of ARS hardly participates in adsorption on HAP. ARS-adsorbed HAP (ARS-HAP) in dark reddish violet was also prepared and analyzed by FT-IR microspectroscopy to gain structural information on bonding between ARS and HAP. The obtained spectrum, which was converted to difference spectra, indicated a single band of nu(C=O) at 1627 cm(-1) and two types of symmetric C=O stretching bands of nu(s)(C=O) + nu(C=C) at 1345 cm(-1) and nu(s)(C=O) + delta(O-C=C) at 1272 cm(-1). These bands imply the existence of a salt form in ARS-HAP via 1-, 2-OH groups of ARS. As a result of the existence of a chelate form in ARS-HAP via 1-OH and 9-C=O groups of ARS, two bands of nu(C=C) + nu(C=O) at 1572 cm(-1) and nu(C=O) + nu(C=C) at 1537 cm(-1) were also observed. In addition, ARS was almost desorbed from colored ARS-HAP at 50 degrees C by using neutral phosphate buffer to recover slightly pale pinkish HAP, or De-ARS-HAP. The desorbed ARS belongs to ARS previously adsorbed on HAP by salt formation, while the remaining color on De-ARS-HAP indicates ARS still adsorbed on HAP by chelate formation. Consequently, we elucidated two adsorption mechanisms of ARS on HAP: The major adsorption is salt formation made up with 1-, 2-O(-) of ARS and Ca2+ on HAP, and the minor adsorption is chelate formation made up with 1-O(-) and 9-C=O of ARS and Ca2+ on HAP.

  4. Synchrotron FTIR microspectroscopy of the yeast Saccharomyces cerevisiae after exposure to plasma-deposited nanosilver-containing coating.

    PubMed

    Saulou, C; Jamme, F; Maranges, C; Fourquaux, I; Despax, B; Raynaud, P; Dumas, P; Mercier-Bonin, M

    2010-02-01

    The present work was focused on elucidating changes in the model yeast Saccharomyces cerevisiae (cell composition, ultrastructure) after exposure to antimicrobial plasma-mediated nanocomposite films. In order to achieve this, a nanosilver-containing coating was deposited onto stainless steel using radiofrequency HMDSO plasma deposition, combined with simultaneous silver sputtering. X-ray photoelectron spectroscopy (XPS) confirmed the presence of silver nanoparticles embedded in an organosilicon matrix. In addition, scanning electron microscopy (SEM) demonstrated the nanoparticle-based morphology of the deposited layer. The antifungal properties towards S. cerevisiae were established, since a 1.4 log reduction in viable counts was observed after a 24-h adhesion compared to control conditions with the matrix alone. Differences in cell composition after exposure to the nanosilver was assessed for the protein region using, for the first time, synchrotron Fourier-transform infrared (FTIR) microspectroscopy of single S. cerevisiae cells, through in situ mapping with sub-cellular spatial resolution. IR spectrum of yeast cells recovered after a 24-h adhesion to the nanosilver-containing coating revealed a significant downshift (20 cm(-1)) of the amide I peak at 1655 cm(-1), compared to freshly harvested cells. This lower band position, corresponding to a loss in alpha-helix structures, is indicative of the disordered secondary structures of proteins, due to the transition between active and inactive conformations under nanosilver-induced stress conditions. No significant effect on the nucleic acid region was detected. The inhibitory action of silver was targeted against both cell wall and intracellular proteins such as enzymes. Transmission electron microscopy (TEM) observations of the yeast ultrastructure confirmed serious morphological and structural damages. A homogeneous protein-binding distribution of nanosilver all over the cell was assumed, since the presence of

  5. Alteration of the bone tissue material properties in type 1 diabetes mellitus: A Fourier transform infrared microspectroscopy study.

    PubMed

    Mieczkowska, Aleksandra; Mansur, Sity Aishah; Irwin, Nigel; Flatt, Peter R; Chappard, Daniel; Mabilleau, Guillaume

    2015-07-01

    Type 1 diabetes mellitus (T1DM) is a severe disorder characterized by hyperglycemia and hypoinsulinemia. A higher occurrence of bone fractures has been reported in T1DM, and although bone mineral density is reduced in this disorder, it is also thought that bone quality may be altered in this chronic pathology. Vibrational microscopies such as Fourier transform infrared microspectroscopy (FTIRM) represent an interesting approach to study bone quality as they allow investigation of the collagen and mineral compartment of the extracellular matrix in a specific bone location. However, as spectral feature arising from the mineral may overlap with those of the organic component, the demineralization of bone sections should be performed for a full investigation of the organic matrix. The aims of the present study were to (i) develop a new approach, based on the demineralization of thin bone tissue section to allow a better characterization of the bone organic component by FTIRM, (ii) to validate collagen glycation and collagen integrity in bone tissue and (iii) to better understand what alterations of tissue material properties in newly forming bone occur in T1DM. The streptozotocin-injected mouse (150 mg/kg body weight, injected at 8 weeks old) was used as T1DM model. Animals were randomly allocated to control (n = 8) or diabetic (n = 10) groups and were sacrificed 4 weeks post-STZ injection. Bones were collected at necropsy, embedded in polymethylmethacrylate and sectioned prior to examination by FTIRM. FTIRM collagen parameters were collagen maturity (area ratio between 1660 and 1690 cm(-1) subbands), collagen glycation (area ratio between the 1032 cm(-1) subband and amide I) and collagen integrity (area ratio between the 1338 cm(-1) subband and amide II). No significant differences in the mineral compartment of the bone matrix could be observed between controls and STZ-injected animals. On the other hand, as compared with controls, STZ-injected animals presented with

  6. Dynamical rate theory of enzymatic reactions and triple-resonant coherent anti-Stokes Raman scattering microspectroscopy

    NASA Astrophysics Data System (ADS)

    Min, Wei

    Chapters 2-7 focus on physical enzymology. Despite its long history, recent single-molecule spectroscopy, among many others techniques, has generated new quantitative data that reveal unobserved features of protein dynamics and enzyme catalysis at unprecedented levels. Much of these are beyond the classic framework of transition state theory and Michalis-Menten (MM) enzyme kinetics. Due to the complexity of the problem, theoretical developments in this area have much lagged behind experiments. After an initial experimental characterization on single-molecule protein conformational fluctuations, we then develop a dynamical rate theory for enzyme catalyzed chemical reactions, from a statistical mechanics approach. Towards this goal, we formulate a two-dimensional (2D) multi-surface free energy description of the entire catalytic process that explicitly combines the concept of "fluctuating enzymes" with the MM enzyme kinetics. The outcome of this framework has two folds. On the rate theory side, going much beyond transition state theory, it connects conformational fluctuations to catalysis, allows for the interplay between energetics (e.g. Haldane's stain energy) and dynamics (e.g. Koshland's induced fit), and predicts the time dependence of single-enzyme catalysis. On the enzyme kinetics side, it gives mechanistic and unified understanding of MM and non-MM (both positive and negative cooperativity) kinetics of monomeric enzymes, in term of non-equilibrium steady state cycle on the 2D free energy surface. Chapters 8-11 present the principle and application of a new ultra-sensitive nonlinear optical microspectroscopy, femtosecond (fs) triple-resonant coherent anti-Stokes Raman scattering (CARS), in which the amplitude and phase of input fs laser pulses are optimally shaped to be in triple resonant with the molecular electronic and vibrational transitions to generate a coherent nonlinear signal beam at a new color with a highest possible efficiency. This technique

  7. Shielding NSLS-II light source: Importance of geometry for calculating radiation levels from beam losses [Shielding Synchrotron Light Sources: Importance of geometry for calculating radiation levels from beam losses

    DOE PAGES

    Kramer, S. L.; Ghosh, V. J.; Breitfeller, M.; ...

    2016-08-10

    Third generation high brightness light sources are designed to have low emittance and high current beams, which contribute to higher beam loss rates that will be compensated by Top-Off injection. Shielding for these higher loss rates will be critical to protect the projected higher occupancy factors for the users. Top-Off injection requires a full energy injector, which will demand greater consideration of the potential abnormal beam miss-steering and localized losses that could occur. The high energy electron injection beam produces significantly higher neutron component dose to the experimental floor than a lower energy beam injection and ramped operations. Minimizing thismore » dose will require adequate knowledge of where the miss-steered beam can occur and sufficient EM shielding close to the loss point, in order to attenuate the energy of the particles in the EM shower below the neutron production threshold (<10 MeV), which will spread the incident energy on the bulk shield walls and thereby the dose penetrating the shield walls. Designing supplemental shielding near the loss point using the analytic shielding model is shown to be inadequate because of its lack of geometry specification for the EM shower process. To predict the dose rates outside the tunnel requires detailed description of the geometry and materials that the beam losses will encounter inside the tunnel. Modern radiation shielding Monte-Carlo codes, like FLUKA, can handle this geometric description of the radiation transport process in sufficient detail, allowing accurate predictions of the dose rates expected and the ability to show weaknesses in the design before a high radiation incident occurs. The effort required to adequately define the accelerator geometry for these codes has been greatly reduced with the implementation of the graphical interface of FLAIR to FLUKA. This made the effective shielding process for NSLS-II quite accurate and reliable. Lastly, the principles used to provide

  8. Plasmon-Based Optical Trapping of Polymer Nano-Spheres as Explored by Confocal Fluorescence Microspectroscopy: A Possible Mechanism of a Resonant Excitation Effect

    NASA Astrophysics Data System (ADS)

    Shoji, Tatsuya; Mizumoto, Yoshihiko; Ishihara, Hajime; Kitamura, Noboru; Takase, Mai; Murakoshi, Kei; Tsuboi, Yasuyuki

    2012-09-01

    In optical trapping using photon force much enhanced by localized surface plasmon (LSP) in solution, we found that a resonant excitation effect can further enhance photon force. In this LSP-based optical trapping under a resonant excitation condition, an incident laser beam excites both LSP and electronic resonant transition of a target object simultaneously. Fluorescence microspectroscopy clearly showed that nanospheres under the resonant condition were much more efficiently trapped as compared to that under a non-resonant condition. The resonant LSP-based trapping mechanism was further reinforced by theoretical calculations taking the resonant excitation effect into account. Such resonant LSP-based trapping methodology will provide a novel approach for efficient trapping of small molecules.

  9. Detection of protein structure of frozen ancient human remains recovered from a glacier in Canada using synchrotron fourier transform infrared microspectroscopy.

    PubMed

    Quaroni, Luca; Christensen, Colleen R; Chen, Becky; Vogl, Wayne; Monsalve, Maria Victoria

    2013-06-01

    We previously used synchrotron infrared microspectroscopy to describe the biochemical signature of skeletal muscle (biceps brachii) from the frozen ancient remains of a young man. In this current paper, we use light microscopy to assess the state of preservation of cellular components in the trapezius muscle from these same ancient remains and then use mid-infrared analysis at the Canadian Light Source synchrotron facility to further analyze the tissue. We compare spectra between the trapezius samples from the ancient remains and a recently deceased cadaver (control). Infrared spectra indicate preservation of secondary structure, with the α-helix being the principal component, along with triple helical portions of the protein backbone. Our mid-infrared analysis indicates an energy reserve in the skeletal muscle in the ancient remains.

  10. Comparison of methodologies for separation of fungal isolates using Fourier transform infrared (FTIR) spectroscopy and Fourier transform infrared-attenuated total reflectance (FTIR-ATR) microspectroscopy.

    PubMed

    Oberle, Jennifer; Dighton, John; Arbuckle-Keil, Georgia

    2015-11-01

    Twenty distinct fungal isolates were analysed using three methods of sample preparation for FTIR spectroscopy and FTIR-ATR microspectroscopy to test for differences in surface chemical composition between living and dried fungal samples, as well as differences between surface chemistry and overall chemistry of homogenized dried samples. Results indicated that visually the FTIR spectra of different fungi are remarkably similar with subtle discernable differences, which statistical analysis of the spectra supported. Within each data set, different fungal isolates were responsible for statistical differences. Lack of congruence between each of the methods used suggests that determination of chemical composition is highly dependent upon the method of sample preparation and analysis (surface vs. whole) applied.

  11. Raman microspectroscopy of noncancerous and cancerous human breast tissues. Identification and phase transitions of linoleic and oleic acids by Raman low-temperature studies.

    PubMed

    Brozek-Pluska, Beata; Kopec, Monika; Surmacki, Jakub; Abramczyk, Halina

    2015-04-07

    We present the results of Raman studies in the temperature range of 293-77 K on vibrational properties of linoleic and oleic acids and Raman microspectroscopy of human breast tissues at room temperature. Our results confirmed the significant role of unsaturated fatty acids in differentiation of noncancerous and cancerous breast tissues and the role of vibrational spectroscopy in phase transition identification. We have found that vibrational properties are very sensitive indicators to specify phases and phase transitions typical of unsaturated fatty acids at the molecular level. Using Raman spectroscopy we have identified high-temperature, middle-temperature and low-temperature phases of linoleic acid. Results obtained for linoleic acid were compared with parameters characteristic of α and γ phases of oleic acid - the parent compound of polyunsaturated fatty acids.

  12. Label-free identification and characterization of murine hair follicle stem cells located in thin tissue sections with Raman micro-spectroscopy.

    PubMed

    Tsai, Tsung-Hua; Short, Michael A; McLean, David I; Zeng, Haishan; McElwee, Kevin; Lui, Harvey

    2014-06-07

    Stem cells offer tremendous opportunities for regenerative medicine. Over the past decade considerable research has taken place to identify and characterize the differentiation states of stem cells in culture. Raman micro-spectroscopy has emerged as an ideal technology since it is fast, nondestructive, and does not require potentially toxic dyes. Raman spectroscopy systems can also be incorporated into confocal microscope imaging systems allowing spectra to be obtained from below the tissue surface. Thus there is significant potential for monitoring stem cells in living tissue. Stem cells that reside in hair follicles are suitable for testing this possibility since they are close to the skin surface, and typically clustered around the bulge area. One of the first steps needed would be to obtain Raman micro-spectra from stem cells located in thin sections of tissue, and then see whether these spectra are clearly different from those of the surrounding differentiated cells. To facilitate this test, standard 5 μm thick sections of murine skin tissue were stained to identify the location of hair follicle stem cells and their progeny. Raman spectra were then obtained from adjacent cells in a subsequent unstained 10 μm thick section. The spectra revealed significant differences in peak intensities associated with nucleic acids, proteins, lipids and amino acids. Statistical analyses of the Raman micro-spectra identified stem cells with 98% sensitivity and 94% specificity, as compared with a CD34 immunostaining gold standard. Furthermore analyses of the spectral variance indicated differences in cellular dynamics between the two cell groups. This study shows that Raman micro-spectroscopy has a potential role in identifying adult follicle stem cells, laying the groundwork for future applications of hair follicle stem cells and other somatic stem cells in situ.

  13. Micas from mariupolite of the Oktiabrski massif (SE Ukraine): An insight into the host rock evolution - Geochemical data supported by Raman microspectroscopy

    NASA Astrophysics Data System (ADS)

    Dumańska-Słowik, Magdalena; Wesełucha-Birczyńska, Aleksandra; Pieczka, Adam

    2015-02-01

    Muscovite and two dark mica varieties (the coarse-crystalline, pegmatitic, and fine-crystalline with signs of early weathering) representing members of the biotite series, originating from mariupolite of the Oktiabrski massif, (Ukraine), were investigated along with their solid inclusions using electron microprobe and Raman micro-spectroscopy to discuss their genesis and relationship to the parental magma. The coarse-crystalline, pegmatitic biotite, (K1.90Rb0.02Na0.01)(Fe2+3.56Mg1.34Ti0.36Fe3+0.34Mn0.03)[(Si5.73Al2.10Fe3+0.17)O20](OH3.24 F0.76) represents the primary, magmatic annite that crystallized from an alkaline, Fe-rich and Mg-depleted host magma, whereas the fine-crystalline biotite, partly altered to vermiculite, (K1.75Rb0.03Na0.03)(Fe3+3.23Fe2+1.16Mg0.26Mn0.04Ti0.10)[(Si5.16 Al2.84)O20](OH)4.00, devoid of F, represents a re-equilibrated or secondary, post-magmatic Fe3+-bearing mica crystallized from alkaline to the subalkaline host magma. Muscovite, (K1.96Na0.06)(Al3.97Fe2+0.06)[(Si5.99Al2.01)O20](OH)4, with low Na/(Na + K) ratio, low Fe and devoid of Ti and also F, forms only tiny, subhedral flakes formed in the post-magmatic, hydrothermal stage. The primary, unaltered biotite contains numerous solid inclusions of primary origin (albite, aegirine, zircon, K-feldspar, nepheline, pyrochlore, magnetite) and secondary origin (natrolite, hematite, Ti-Mn oxides/hydroxides); most of them are accompanied by a carbonaceous substance, all confirmed by scanning electron microscopy and Raman microspectroscopy.

  14. Study of cell-differentiation and assembly of photosynthetic proteins during greening of etiolated Zea mays leaves using confocal fluorescence microspectroscopy at liquid-nitrogen temperature.

    PubMed

    Shibata, Yutaka; Katoh, Wataru; Tahara, Yukari

    2013-04-01

    Fluorescence microspectroscopy observations were used to study the processes of cell differentiation and assemblies of photosynthesis proteins in Zea mays leaves under the greening process. The observations were done at 78K by setting the sample in a cryostat to avoid any undesired progress of the greening process during the measurements. The lateral and axial spatial resolutions of the system were 0.64μm and 4.4μm, respectively. The study revealed the spatial distributions of protochlorophyllide (PChld) in both the 632-nm-emitting and 655-nm-emitting forms within etiolated Zea mays leaves. The sizes of the fluorescence spots attributed to the former were larger than those of the latter, validating the assignment of the former and latter to the prothylakoid and prolamellar bodies, respectively. In vivo microspectroscopy observations of mature Zea mays leaves confirmed the different photosystem II (PS I)/photosystem I (PS II) ratio between the bundle sheath (BS) and mesophyll (MS) cells, which is specific for C4-plants. The BS cells in Zea mays leaves 1h after the initiation of the greening process tended to show fluorescence spectra at shorter wavelength side (at around 679nm) than the MS cells (at around 682nm). The 679-nm-emitting chlorophyll-a form observed mainly in the BS cells was attributed to putative precursor complexes to PS I. The BS cells under 3-h greening showed higher relative intensities of the PS I fluorescence band at around 735nm, suggesting the reduced PS II amount in the BS cells in this greening stage. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. High-spatial-resolution mapping of superhydrophobic cicada wing surface chemistry using infrared microspectroscopy and infrared imaging at two synchrotron beamlines.

    PubMed

    Tobin, Mark J; Puskar, Ljiljana; Hasan, Jafar; Webb, Hayden K; Hirschmugl, Carol J; Nasse, Michael J; Gervinskas, Gediminas; Juodkazis, Saulius; Watson, Gregory S; Watson, Jolanta A; Crawford, Russell J; Ivanova, Elena P

    2013-05-01

    The wings of some insects, such as cicadae, have been reported to possess a number of interesting and unusual qualities such as superhydrophobicity, anisotropic wetting and antibacterial properties. Here, the chemical composition of the wings of the Clanger cicada (Psaltoda claripennis) were characterized using infrared (IR) microspectroscopy. In addition, the data generated from two separate synchrotron IR facilities, the Australian Synchrotron Infrared Microspectroscopy beamline (AS-IRM) and the Synchrotron Radiation Center (SRC), University of Wisconsin-Madison, IRENI beamline, were analysed and compared. Characteristic peaks in the IR spectra of the wings were assigned primarily to aliphatic hydrocarbon and amide functionalities, which were considered to be an indication of the presence of waxy and proteinaceous components, respectively, in good agreement with the literature. Chemical distribution maps showed that, while the protein component was homogeneously distributed, a significant degree of heterogeneity was observed in the distribution of the waxy component, which may contribute to the self-cleaning and aerodynamic properties of the cicada wing. When comparing the data generated from the two beamlines, it was determined that the SRC IRENI beamline was capable of producing higher-spatial-resolution distribution images in a shorter time than was achievable at the AS-IRM beamline, but that spectral noise levels per pixel were considerably lower on the AS-IRM beamline, resulting in more favourable data where the detection of weak absorbances is required. The data generated by the two complementary synchrotron IR methods on the chemical composition of cicada wings will be immensely useful in understanding their unusual properties with a view to reproducing their characteristics in, for example, industry applications.

  16. Analysis Of Pulmonary Tissue Of Natural Mummy Of XIII Century (Saint Zita, Lucca-Tuscany) By Means Of FT-IR Microspectroscopy.

    NASA Astrophysics Data System (ADS)

    Benedetti, Enzo; Vergamini, Piergiorgio; Fornaciari, Gino; Spremolla, Giuliano

    1989-12-01

    During a recognition carried out by one of us on the S.Zita's body, preserved for seven hundred years in the S.Frediano's Basilica (Lucca, Tuscany-Italy) it has been possible to verify the good condition of many orgains and systems. In this comunication we report preliminary results of an analysis of the pulmonary tissue which to the histologic examination showed a typical aspect. It was observed the presence of a massive anthracosis. In order to obtain indication, at molecular level, FT-IR microspectroscopy measurements were carried out. The infrared spectra relative to different microareas allowed us to evidence regions of tissue decomposed, and others in which the infrared spectra showed absorptions characteristic of proteic components at 1650 cm-1 and 1540 cm-1 ascribed to the Amide I and Amide II vibrations respectively. In the 1350-950 cm-1 range bands due to nucleic acids were detected. Also in the CH stretching region bands due to methyl and methylene groups were observed, likely due to the presence of paraffinic segments of phospholipids of cellular membranes. Previous FT-IR studies carried out by us on biological systems such as normal and leukemic lymphocytes (1), on lymphoblast (2), and recently on cells isolated from neoplastic pulmonary tissues (3), represent a basis which allows us to perform a sufficiently complete assignment on the spectra obtained on this finding. These spectra are surprisingly very similar to those obtained by us on human lung tissue from surgical specimens. As far as we know, FT-IR microspectroscopy, which was first employed by our group in the study of human neoplasia at level of single cell (4) has been applied in the analysis of ancient pulmonary tissue, certainly not submitted to any conservative treatment. This kind of approach can open up new possibilities in obtaining indication, at molecular level, on findings of paleophanthology of different origin and age.

  17. Monitoring doxorubicin cellular uptake and trafficking using in vitro Raman microspectroscopy: short and long time exposure effects on lung cancer cell lines.

    PubMed

    Farhane, Zeineb; Bonnier, Franck; Byrne, Hugh J

    2017-02-01

    Raman microspectroscopy is a non-invasive, in vitro analytical tool which is being increasingly explored for its potential in clinical applications and monitoring the uptake, mechanism of action and cellular interaction at a molecular level of chemotherapeutic drugs, ultimately as a potential label-free preclinical screening and companion diagnostic tool. In this study, doxorubicin (DOX), a "gold standard" chemotherapeutic drug, is employed as a model in the in vitro lung cancer cell line A549 in order to demonstrate the potential of Raman microspectroscopy to screen and identify spectroscopic markers of its trafficking and mechanism of action. Confocal laser scanning microscopy (CLSM) was used in parallel to illustrate the uptake and subcellular localisation, and cytotoxicity assays were employed to establish the toxicity profiles for early and late exposure times of A549 to DOX. Multivariate statistical analysis, consisting of principal components analysis (PCA), partial least squares regression (PLSR) and independent component analysis (ICA), was used to elucidate the spectroscopic signatures associated with DOX uptake and subcellular interaction. Raman spectroscopic profiling illustrates both drug kinetics and its pharmacodynamics in the cell and associated biochemical changes, demonstrating that DOX is mainly localised in the nuclear area, saturating the nucleolus first, within ~6 h of exposure, before the surrounding nuclear areas after ~12 h, and only accumulates in the cytoplasm after 48 h. PLSR over varying time intervals enables identification of DOX-DNA binding at early stages of exposure (0-12 h), while regression over longer time periods (24-72 h) reveals spectroscopic signatures associated with the metabolic cellular response. Graphical Abstract Subcellular uptake of doxorubicin, and changes in biomolecular signatures in the nucleolus, as monitored by Raman spectroscopy.

  18. Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms.

    PubMed

    Reuben, Sheela; Banas, Krzysztof; Banas, Agnieszka; Swarup, Sanjay

    2014-11-01

    Understanding the spatial heterogeneity within environmental biofilms can provide an insight into compartmentalization of different functions in biofilm communities. We used a non-destructive and label-free method by combining Synchrotron Radiation-based Fourier Transform Infrared Microspectroscopy (SR-FTIR) with Confocal Laser Scanning Microscopy (CLSM) to distinguish the spatial chemical changes within multispecies biofilms grown from natural storm waters in flow cells. Among the different surfaces tested for biofilm growth and optimal imaging, mylar membranes were most suited and it enabled successful spatial infrared imaging of natural biofilms for obtaining reliable and interpretable FTIR spectra. Time series analysis of biofilm growth showed that influx of water during biofilm growth, results in significant changes in biofilm formation. Early biofilms showed active nutrient acquisition and desiccation tolerance mechanisms corresponding with accumulation of secreted proteins. Statistical approach used for the evaluation of chemical spectra allowed for clustering and classification of various regions of the biofilm. Microheterogeneity was observed in the polymeric components of the biofilm matrix, including cellulose, glycocalyx and dextran-like molecules. Fructan and glycan-rich regions were distinguishable and glycocalyx was abundant in the strongly adhering peripheral regions of biofilms. Inner core showed coexistence of oxygen dimers and ferrihydrite that will likely support growth of Fe (II)-oxidising bacteria. The combined SR-FTIR microspectroscopy and CSLM approach for complex natural biofilms described here will be useful both in understanding heterogeneity of matrix components and in correlating functions of juxtaposed microbial species in complex natural biofilms with physicochemical microenvironment to which they are exposed.

  19. Community Plan for Far-Infared/Submillimeter Space Astronomy

    NASA Technical Reports Server (NTRS)

    Leisawitz, David; Oegerle, William (Technical Monitor)

    2003-01-01

    The consensus of attendees at the Second Workshop on New Concepts for Far-Infrared/Submillimeter Space Astronomy is that the Single Aperture Far-IR telescope (SAFIR), a cooled spaceborne observatory, is important for the future of far-infrared astronomy. This paper describes the specifications and capabilities of SAFIR, possible designs for SAFIR, and suggests a development strategy for the technology necessary for the telescope.

  20. FORCAST: the faint object infared camera for the SOFIA telescope

    NASA Astrophysics Data System (ADS)

    Keller, Luke D.; Herter, Terry L.; Stacey, Gordon J.; Gull, George E.; Schoenwald, Justin; Pirger, Bruce; Nikola, Tomas

    2003-02-01

    We report final design details and development progress for the Faint Object Infrared Camera for the SOFIA Telescope (FORCAST). FORCAST is a two-channel camera with selectable filters for continuum and line imaging in the 5-40 micron wavelength region. Simultaneous imaging will be possible in the two-channels--5-25 microns using a Si:As 256×256 blocked impurity band (BIB) detector array, and 25-40 microns using a Si:Sb BIB. FORCAST will sample 0.75 arcseconds per pixel allowing a 3.2'×3.2' instantaneous field-of-view in both channels simultaneously. Imaging will be diffraction limited for lambda > 15 microns. Since FORCAST operates in the wavelength range where the seeing is best from SOFIA, it will provide the highest spatial resolution possible from the airborne observatory. In addition to imaging, the FORCAST optical design provides for a simple upgrade to include spectroscopic observations using grisms mounted in the filter wheels. We report improvements to the optical system and progress in construction of this SOFIA facility instrument and its subsystems. FORCAST will be available for facility testing and astronomical observations at SOFIA first (f)light.